Merge branch 'develop' into collected-small-changes

cmake/Modules/StyleHeaderUtils.cmake

@@ -95,73 +95,76 @@ function(RegisterIntegrateStyle path)
 endfunction(RegisterIntegrateStyle)
 
 function(RegisterStyles search_path)
-    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
-    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
-    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
-    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
-    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
-    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
-    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
-    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
-    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
-    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
-    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
-    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
-    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
-    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
-    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
-    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
-    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+    FindStyleHeaders(${search_path} ANGLE_CLASS        angle_        ANGLE        ) # angle        ) # force
+    FindStyleHeaders(${search_path} ATOM_CLASS         atom_vec_     ATOM_VEC     ) # atom         ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} BODY_CLASS         body_         BODY         ) # body         ) # atom_vec_body
+    FindStyleHeaders(${search_path} BOND_CLASS         bond_         BOND         ) # bond         ) # force
+    FindStyleHeaders(${search_path} COMMAND_CLASS      "[^.]"        COMMAND      ) # command      ) # input
+    FindStyleHeaders(${search_path} COMPUTE_CLASS      compute_      COMPUTE      ) # compute      ) # modify
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS     dihedral_     DIHEDRAL     ) # dihedral     ) # force
+    FindStyleHeaders(${search_path} DUMP_CLASS         dump_         DUMP         ) # dump         ) # output    write_dump
+    FindStyleHeaders(${search_path} FIX_CLASS          fix_          FIX          ) # fix          ) # modify
+    FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
+    FindStyleHeaders(${search_path} IMPROPER_CLASS     improper_     IMPROPER     ) # improper     ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS    "[^.]"        INTEGRATE    ) # integrate    ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS       "[^.]"        KSPACE       ) # kspace       ) # force
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS     min_          MINIMIZE     ) # minimize     ) # update
+    FindStyleHeaders(${search_path} NBIN_CLASS         nbin_         NBIN         ) # nbin         ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS        npair_        NPAIR        ) # npair        ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS     nstencil_     NSTENCIL     ) # nstencil     ) # neighbor
+    FindStyleHeaders(${search_path} NTOPO_CLASS        ntopo_        NTOPO        ) # ntopo        ) # neighbor
+    FindStyleHeaders(${search_path} PAIR_CLASS         pair_         PAIR         ) # pair         ) # force
+    FindStyleHeaders(${search_path} READER_CLASS       reader_       READER       ) # reader       ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS       region_       REGION       ) # region       ) # domain
 endfunction(RegisterStyles)
 
 function(RegisterStylesExt search_path extension sources)
-    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
-    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
-    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
-    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
-    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
-    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
-    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
-    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
-    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
-    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
-    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
-    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
-    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
-    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
-    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
-    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
-    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
-    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
-    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
-    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS        ${extension}  ANGLE        ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS         ${extension}  ATOM_VEC     ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS         ${extension}  BODY         ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS         ${extension}  BOND         ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS      ${extension}  COMMAND      ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS      ${extension}  COMPUTE      ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS     ${extension}  DIHEDRAL     ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS         ${extension}  DUMP         ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS          ${extension}  FIX          ${sources})
+    FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension}  GRAN_SUB_MOD ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS     ${extension}  IMPROPER     ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS    ${extension}  INTEGRATE    ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS       ${extension}  KSPACE       ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS     ${extension}  MINIMIZE     ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS         ${extension}  NBIN         ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS        ${extension}  NPAIR        ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS     ${extension}  NSTENCIL     ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS        ${extension}  NTOPO        ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS         ${extension}  PAIR         ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS       ${extension}  READER       ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS       ${extension}  REGION       ${sources})
 endfunction(RegisterStylesExt)
 
 function(GenerateStyleHeaders output_path)
     message(STATUS "Generating style headers...")
-    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
-    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
-    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
-    GenerateStyleHeader(${output_path} BOND       bond      ) # force
-    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
-    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
-    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
-    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
-    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
-    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
-    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
-    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
-    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
-    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
-    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
-    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
-    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
-    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
-    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
-    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+    GenerateStyleHeader(${output_path} ANGLE        angle        ) # force
+    GenerateStyleHeader(${output_path} ATOM_VEC     atom         ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} BODY         body         ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BOND         bond         ) # force
+    GenerateStyleHeader(${output_path} COMMAND      command      ) # input
+    GenerateStyleHeader(${output_path} COMPUTE      compute      ) # modify
+    GenerateStyleHeader(${output_path} DIHEDRAL     dihedral     ) # force
+    GenerateStyleHeader(${output_path} DUMP         dump         ) # output    write_dump
+    GenerateStyleHeader(${output_path} FIX          fix          ) # modify
+    GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
+    GenerateStyleHeader(${output_path} IMPROPER     improper     ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE    integrate    ) # update
+    GenerateStyleHeader(${output_path} KSPACE       kspace       ) # force
+    GenerateStyleHeader(${output_path} MINIMIZE     minimize     ) # update
+    GenerateStyleHeader(${output_path} NBIN         nbin         ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR        npair        ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL     nstencil     ) # neighbor
+    GenerateStyleHeader(${output_path} NTOPO        ntopo        ) # neighbor
+    GenerateStyleHeader(${output_path} PAIR         pair         ) # force
+    GenerateStyleHeader(${output_path} READER       reader       ) # read_dump
+    GenerateStyleHeader(${output_path} REGION       region       ) # domain
 endfunction(GenerateStyleHeaders)
 
 function(DetectBuildSystemConflict lammps_src_dir)

doc/src/Commands_fix.rst

@@ -94,6 +94,7 @@ OPT.
    * :doc:`grem <fix_grem>`
    * :doc:`halt <fix_halt>`
    * :doc:`heat <fix_heat>`
+   * :doc:`heat/flow <fix_heat_flow>`
    * :doc:`hyper/global <fix_hyper_global>`
    * :doc:`hyper/local <fix_hyper_local>`
    * :doc:`imd <fix_imd>`

doc/src/Howto_granular.rst

@@ -43,6 +43,15 @@ The fix style *freeze* zeroes both the force and torque of frozen
 atoms, and should be used for granular system instead of the fix style
 *setforce*\ .
 
+To model heat conduction, one must add the temperature and heatflow
+atom variables with:
+* :doc:`fix property/atom <fix_property_atom>`
+a temperature integration fix
+* :doc:`fix heat/flow <fix_heat_flow>`
+and a heat conduction option defined in both
+* :doc:`pair_style granular <pair_granular>`
+* :doc:`fix wall/gran <fix_wall_gran>`
+
 For computational efficiency, you can eliminate needless pairwise
 computations between frozen atoms by using this command:
 
@@ -55,3 +64,6 @@ computations between frozen atoms by using this command:
    will be the same as in 3d.  If you wish to model granular particles in
    2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
    doc page, where 2d simulations are discussed.
+
+To add custom granular contact models, see the
+:doc:`modifying granular sub-models page <Modify_gran_sub_mod>`.

doc/src/Modify.rst

@@ -34,5 +34,6 @@ style requirements and recommendations <Modify_style>`.
    Modify_min
    Modify_region
    Modify_body
+   Modify_gran_sub_mod
    Modify_thermo
    Modify_variable

doc/src/Modify_gran_sub_mod.rst

@@ -0,0 +1,177 @@
+Granular Sub-Model styles
+===============================
+
+In granular models, particles are spheres with a finite radius and rotational
+degrees of freedom as further described in the
+:doc:`Howto granular page <Howto_granular>`. Interactions between pair of
+particles or particles and walls may therefore depend on many different modes
+of motion as described in :doc:`pair granular <pair_granular>` and
+:doc:`fix wall/gran <fix_wall_gran>`. In both cases, the exchange of forces,
+torques, and heat flow between two types of bodies is defined using a
+GranularModel class. The GranularModel class organizes the details of an
+interaction using a series of granular sub-models each of which describe a
+particular interaction mode (e.g. normal forces or rolling friction). From a
+parent GranSubMod class, several types of sub-model classes are derived:
+
+* GranSubModNormal: normal force sub-model
+* GranSubModDamping: normal damping sub-model
+* GranSubModTangential: tangential forces and sliding friction sub-model
+* GranSubModRolling: rolling friction sub-model
+* GranSubModTwisting: twisting friction sub-model
+* GranSubModHeat: heat conduction sub-model
+
+For each type of sub-model, more classes are further derived, each describing
+a specific implementation. For instance, from the GranSubModNormal class the
+GranSubModNormalHooke, GranSubModNormalHertz, and GranSubModNormalJKR classes
+are derived which calculate Hookean, Hertzian, or JKR normal forces, respectively.
+This modular structure simplifies the addition of new granular contact models as
+as one onlyneeds to create a new GranSubMod class without having to modify the more
+complex PairGranular, FixGranWall, and GranularModel classes. Most GranSubMod methods
+are also already defined by the parent classes so new contact models typically only
+require edits to a few relevant methods (e.g. methods that define coefficients and
+calculate forces).
+
+Each GranSubMod class has a pointer to both the LAMMPS class and the GranularModel
+class which owns it, ``lmp`` and ``gm``, respectively. The GranularModel class
+includes several public variables that describe the geometry/dynamics of the
+contact such as
+
+.. list-table::
+
+   * - ``xi`` and ``xj``
+     - Positions of the two contacting bodies
+   * - ``vi`` and ``vj``
+     - Velocities of the two contacting bodies
+   * - ``omegai`` and ``omegaj``
+     - Angular velocities of the two contacting bodies
+   * - ``dx`` and ``nx``
+     - The displacement and normalized displacement vectors
+   * - ``r``, ``rsq``, and ``rinv``
+     - The distance, distance squared, and inverse distance
+   * - ``radsum``
+     - The sum of particle radii
+   * - ``vr``, ``vn``, and ``vt``
+     - The relative velocity vector and its normal and tangential components
+   * - ``wr``
+     - The relative rotational velocity
+
+These quantities, among others, are calculated in the ``GranularModel->check_contact()``
+and ``GranularModel->calculate_forces()`` methods which can be referred to for more
+details.
+
+To create a new GranSubMod class, it is recommended that one first looks at similar
+GranSubMod classes. All GranSubMod classes share several general methods which may
+need to be defined
+
+.. list-table::
+
+   * - ``GranSubMod->mix_coeff()``
+     - Optional method to define how coefficients are mixed for different atom types. By default, coefficients are mixed using a geometric mean.
+   * - ``GranSubMod->coeffs_to_local()``
+     - Parses coefficients to define local variables. Run once at model construction.
+   * - ``GranSubMod->init()``
+     - Optional method to define local variables after other GranSubMod types were created. For instance, this method may be used by a tangential model that derives parameters from the normal model.
+
+There are also several type-specific methods
+
+.. list-table::
+
+   * - ``GranSubModNormal->touch()``
+     - Optional method to test when particles are in contact. By default, this is when particles overlap.
+   * - ``GranSubModNormal->pulloff_distance()``
+     - Optional method to return the distance at which particles stop interacting. By default, this is when particles no longer overlap.
+   * - ``GranSubModNormal->calculate_area()``
+     - Optional method to return the surface area of the contact. By default, this returns the geometric cross section.
+   * - ``GranSubModNormal->set_fncrit()``
+     - Optional method that defines the critical force to break the contact used by some tangential, rolling, and twisting sub-models. By default, this is the current total normal force including damping.
+   * - ``GranSubModNormal->calculate_forces()``
+     - Required method that returns the normal contact force
+   * - ``GranSubModDamping->calculate_forces()``
+     - Required method that returns the normal damping force
+   * - ``GranSubModTangential->calculate_forces()``
+     - Required method that calculates tangential forces/torques
+   * - ``GranSubModTwisting->calculate_forces()``
+     - Required method that calculates twisting friction forces/torques
+   * - ``GranSubModRolling->calculate_forces()``
+     - Required method that calculates rolling friction forces/torques
+   * - ``GranSubModHeat->calculate_heat()``
+     - Required method that returns the rate of heat flow
+
+As an example, say one wanted to create a new normal force option that consisted
+of a Hookean force with a piecewise stiffness. This could be done by adding a new
+set of files ``gran_sub_mod_custom.h``:
+
+.. code-block:: c++
+
+   #ifdef GranSubMod_CLASS
+   // clang-format off
+   GranSubModStyle(hooke/piecewise,
+            GranSubModNormalHookePiecewise,
+            NORMAL);
+   // clang-format on
+   #else
+
+   #ifndef GRAN_SUB_MOD_CUSTOM_H_
+   #define GRAN_SUB_MOD_CUSTOM_H_
+
+   #include "gran_sub_mod.h"
+   #include "gran_sub_mod_normal.h"
+
+   namespace LAMMPS_NS {
+   namespace Granular_NS {
+
+   class GranSubModNormalHookePiecewise : public GranSubModNormal {
+    public:
+     GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
+     void coeffs_to_local() override;
+     double calculate_forces();
+    protected:
+     double k1, k2, delta_switch;
+   };
+
+   }    // namespace Granular_NS
+   }    // namespace LAMMPS_NS
+
+   #endif /*GRAN_SUB_MOD_CUSTOM_H_ */
+   #endif /*GRAN_SUB_MOD_CLASS_H_ */
+
+
+and ``gran_sub_mod_custom.cpp``
+
+.. code-block:: c++
+
+   #include "gran_sub_mod_custom.h"
+   #include "gran_sub_mod_normal.h"
+   #include "granular_model.h"
+
+   using namespace LAMMPS_NS;
+   using namespace Granular_NS;
+
+   GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) :  GranSubModNormal(gm, lmp)
+   {
+     num_coeffs = 4;
+   }
+
+   /* ---------------------------------------------------------------------- */
+
+   void GranSubModNormalHookePiecewise::coeffs_to_local()
+   {
+     k1 = coeffs[0];
+     k2 = coeffs[1];
+     damp = coeffs[2];
+     delta_switch = coeffs[3];
+   }
+
+   /* ---------------------------------------------------------------------- */
+
+   double GranSubModNormalHookePiecewise::calculate_forces()
+   {
+     double Fne;
+     if (gm->delta >= delta_switch) {
+       Fne = k1 * delta_switch + k2 * (gm->delta - delta_switch);
+     } else {
+       Fne = k1 * gm->delta;
+     }
+     return Fne;
+   }
+

doc/src/atom_style.rst

@@ -161,15 +161,14 @@ and each stores a per-particle diameter and mass.  If the diameter >
 0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
 is a point particle.  Note that by use of the *disc* keyword with the
 :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
-<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
-npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
-can be effectively treated as 2d discs for a 2d simulation if desired.
-See also the :doc:`set density/disc <set>` command.  The *sphere* and
-*bpm/sphere* styles take an optional 0 or 1 argument.  A value of 0
-means the radius of each sphere is constant for the duration of the
-simulation.  A value of 1 means the radii may vary dynamically during
-the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
-command.
+<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
+:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
+spheres can be effectively treated as 2d discs for a 2d simulation if
+desired.  See also the :doc:`set density/disc <set>` command.  These
+styles take an optional 0 or 1 argument.  A value of 0 means the
+radius of each sphere is constant for the duration of the simulation.
+A value of 1 means the radii may vary dynamically during the simulation,
+e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
 
 For the *ellipsoid* style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or

doc/src/dump.rst

@@ -111,6 +111,7 @@ Syntax
                                q, mux, muy, muz, mu,
                                radius, diameter, omegax, omegay, omegaz,
                                angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                               heatflow, temperature,
                                c_ID, c_ID[I], f_ID, f_ID[I], v_name,
                                i_name, d_name, i2_name[I], d2_name[I]
 
@@ -133,10 +134,12 @@ Syntax
            q = atom charge
            mux,muy,muz = orientation of dipole moment of atom
            mu = magnitude of dipole moment of atom
-           radius,diameter = radius,diameter of spherical particle
+           radius,diameter = radius, diameter of spherical particle
            omegax,omegay,omegaz = angular velocity of spherical particle
            angmomx,angmomy,angmomz = angular momentum of aspherical particle
            tqx,tqy,tqz = torque on finite-size particles
+           heatflow = rate of heat flow into particle
+           temperature = temperature of particle
            c_ID = per-atom vector calculated by a compute with ID
            c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
            f_ID = per-atom vector calculated by a fix with ID

doc/src/fix.rst

@@ -246,6 +246,7 @@ accelerated styles exist.
 * :doc:`grem <fix_grem>` - implements the generalized replica exchange method
 * :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
 * :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
+* :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
 * :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
 * :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
 * :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol

doc/src/fix_heat_flow.rst

@@ -0,0 +1,70 @@
+.. index:: fix heat/flow
+
+fix heat/flow command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID heat/flow style values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* heat/flow = style name of this fix command
+* one style with corresponding value(s) needs to be listed
+
+  .. parsed-literal::
+
+     style = *constant* or *type*
+       *constant* = cp
+         cp = value of specifc heat (energy/(mass * temperature) units)
+       *type* = cp1 ... cpN
+         cpN = value of specifc heat for type N (energy/(mass * temperature) units)
+
+*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all heat/flow constant 1.0
+   fix 1 all heat/flow type 1.0 0.5
+
+Description
+"""""""""""
+
+Perform plain time integration to update temperature for atoms in the
+group each timestep. The specific heat of atoms can be defined using either
+the *constant* or *type* keywords. For style *constant*, the specific heat
+is a constant value *cp* for all atoms. For style *type*, *N* different values
+of the specific heat are defined, one for each of the *N* types of atoms.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+No global or per-atom quantities are stored by this fix for access by various
+:doc:`output commands <Howto_output>`. No parameter of this fix can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  This fix is
+not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+This fix requires that atoms store temperature and heat flow
+as defined by the :doc:`fix property/atom <fix_property_atom>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
+
+Default
+"""""""
+
+none

doc/src/fix_wall_gran.rst

@@ -46,7 +46,7 @@ Syntax
          radius = cylinder radius (distance units)
 
 * zero or more keyword/value pairs may be appended to args
-* keyword = *wiggle* or *shear* or *contacts*
+* keyword = *wiggle* or *shear* or *contacts* or *temperature*
 
   .. parsed-literal::
 
@@ -59,6 +59,8 @@ Syntax
          vshear = magnitude of shear velocity (velocity units)
       *contacts* value = none
          generate contact information for each particle
+      *temperature* value = temperature
+         specify temperature of wall
 
 
 Examples
@@ -71,7 +73,7 @@ Examples
    fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
-   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji heat 10 region myCone temperature 1.0
    fix 6 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
 
 Description
@@ -177,6 +179,16 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
 *vshear* < 0.  In this case, *vshear* is the tangential velocity of
 the wall at whatever *radius* has been defined.
 
+The *temperature* keyword is used to assign a temperature to the wall.
+The following value can either be a numeric value or an equal-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each timestep, and its value used to determine
+the temperature. This option must be used in conjunction with a heat
+conduction model defined in :doc:`pair_style granular <pair_granular>`,
+:doc:`fix property/atom <fix_property_atom>` to store temperature and a
+heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
+flow.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

doc/src/fix_wall_gran_region.rst

@@ -36,12 +36,14 @@ Syntax
 
 * wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
 * region-ID = region whose boundary will act as wall
-* keyword = *contacts*
+* keyword = *contacts* or *temperature*
 
   .. parsed-literal::
 
       *contacts* value = none
          generate contact information for each particle
+      *temperature* value = temperature
+         specify temperature of wall
 
 Examples
 """"""""
@@ -200,6 +202,17 @@ values for the 6 wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
 material.
 
+The *temperature* keyword is used to assign a temperature to the wall.
+The following value can either be a numeric value or an equal-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each timestep, and its value used to determine
+the temperature. This option must be used in conjunction with a heat
+conduction model defined in :doc:`pair_style granular <pair_granular>`,
+:doc:`fix property/atom <fix_property_atom>` to store temperature and a
+heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
+flow.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_gran.rst

@@ -279,6 +279,11 @@ statistically similar results.  This is because the forces they
 compute depend on atom velocities.  See the
 :doc:`read_restart <read_restart>` command for more details.
 
+Accumulated values for individual contacts are saved to to restart
+files but are not saved to data files. Therefore, forces may
+differ significantly when a system is reloaded using A
+:doc:`read_data <read_data>` command.
+
 Related commands
 """"""""""""""""
 

doc/src/pair_granular.rst

@@ -37,6 +37,9 @@ Examples
    pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
    pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
 
+   pair_style granular
+   pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 heat area 0.1
+
 Description
 """""""""""
 
@@ -223,16 +226,19 @@ for all models except *jkr*, for which it is given implicitly according
 to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`.  For *damping viscoelastic*,
 :math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
 
-The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`. Here, the damping coefficient specified as part of
-the normal model is interpreted as a restitution coefficient
-:math:`e`. The damping constant :math:`\eta_n` is given by:
+The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`.
+Here, the damping coefficient specified as part of the normal model is interpreted
+as a restitution coefficient :math:`e`. The damping constant :math:`\eta_n` is
+given by:
 
 .. math::
 
    \eta_n = \alpha (m_{eff}k_n)^{1/2}
 
-For normal contact models based on material parameters, :math:`k_n = 4/3Ea`.  The parameter :math:`\alpha` is related to the restitution
-coefficient *e* according to:
+For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. This
+damping model is not compatible with cohesive normal models such as *JKR* or *DMT*.
+The parameter :math:`\alpha` is related to the restitution coefficient *e*
+according to:
 
 .. math::
 
@@ -631,6 +637,34 @@ attractive force. This keyword cannot be used with the JKR or DMT models.
 
 ----------
 
+The optional *heat* keyword enables heat conduction. The options currently
+supported are:
+
+1. *none*
+2. *area* : :math:`k_{s}`
+
+If the *heat* keyword is not specified, the model defaults to *none*.
+
+For *heat* *area*, the heat
+:math:`Q` conducted between two particles is given by
+
+.. math::
+
+   Q = k_{s} a \Delta T
+
+
+
+where :math:`\Delta T` is the difference in the two particles' temperature,
+:math:`k_{s}` is a non-negative numeric value for the conductivity, and
+:math:`a` is the area of the contact and depends on the normal force model.
+
+Note that the option *none* must either be used in all or none of of the
+*pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and
+:doc:`fix property/atom <fix_property_atom>` for more information on this
+option.
+
+----------
+
 The *granular* pair style can reproduce the behavior of the
 *pair gran/\** styles with the appropriate settings (some very
 minor differences can be expected due to corrections in
@@ -641,7 +675,7 @@ is equivalent to *pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1*\ .
 The second example is equivalent to
 *pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
 The third example is equivalent to
-*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
+*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1 limit_damping*\ .
 
 ----------
 
@@ -733,22 +767,30 @@ These extra quantities can be accessed by the :doc:`compute pair/local <compute_
 Restrictions
 """"""""""""
 
-All the granular pair styles are part of the GRANULAR package.  It is
-only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+This pair style is part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
 
-These pair styles require that atoms store torque and angular velocity
-(omega) as defined by the :doc:`atom_style <atom_style>`.  They also
-require a per-particle radius is stored.  The *sphere* atom style does
-all of this.
+This pair style requires that atoms store per-particle radius,
+torque, and angular velocity (omega) as defined by the
+:doc:`atom_style sphere <atom_style>`.
 
-This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost
-atoms.
+This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>`
+command so that velocities are stored by ghost atoms.
 
-These pair styles will not restart exactly when using the
-:doc:`read_restart <read_restart>` command, though they should provide
-statistically similar results.  This is because the forces they
-compute depend on atom velocities.  See the
-:doc:`read_restart <read_restart>` command for more details.
+This pair style will not restart exactly when using the
+:doc:`read_restart <read_restart>` command, though it should provide
+statistically similar results.  This is because the forces it
+computes depend on atom velocities and the atom velocities have
+been propagated half a timestep between the force computation and
+when the restart is written, due to using Velocity Verlet time
+integration. See the :doc:`read_restart <read_restart>` command
+for more details.
+
+Accumulated values for individual contacts are saved to restart
+files but are not saved to data files. Therefore, forces may
+differ significantly when a system is reloaded using the
+:doc:`read_data <read_data>` command.
 
 Related commands
 """"""""""""""""

doc/src/set.rst

@@ -19,7 +19,7 @@ Syntax
   *spin/electron* or *radius/electron* or
   *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
   *theta* or *theta/random* or *angmom* or *omega* or
-  *mass* or *density* or *density/disc* or
+  *mass* or *density* or *density/disc* or *temperature* or
   *volume* or *image* or *bond* or *angle* or *dihedral* or
   *improper* or *sph/e* or *sph/cv* or *sph/rho* or
   *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
@@ -100,6 +100,8 @@ Syntax
          value can be an atom-style variable (see below)
        *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
          value can be an atom-style variable (see below)
+       *temperature* value = temperature for finite-size particles (temperature units)
+         value can be an atom-style variable (see below)
        *volume* value = particle volume for Peridynamic particle (distance\^3 units)
          value can be an atom-style variable (see below)
        *image* nx ny nz
@@ -429,6 +431,12 @@ assumed to be in mass/distance\^2 units).
 If none of these cases are valid, then the mass is set to the density
 value directly (the input density is assumed to be in mass units).
 
+Keyword *temperature* sets the temperature of a finite-size particle.
+Currently, only the GRANULAR package supports this attribute. The
+temperature must be added using an instance of
+:doc:`fix property/atom <fix_property_atom>` The values for the
+temperature must be positive.
+
 Keyword *volume* sets the volume of all selected particles.  Currently,
 only the :doc:`atom_style peri <atom_style>` command defines particles
 with a volume attribute.  Note that this command does not adjust the

doc/utils/sphinx-config/false_positives.txt

@@ -1372,6 +1372,7 @@ hdnnp
 HDNNP
 Hearn
 heatconduction
+heatflow
 Hebbeker
 Hebenstreit
 Hecht

examples/granregion/log.15Sep22.granregion.box.g++.1

@@ -0,0 +1,493 @@
+LAMMPS (15 Sep 2022)
+# pouring spheres into container box
+
+units		lj
+atom_style      sphere
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -10 10 -10 10 -10 10 units box
+create_box      2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* * gran/hooke
+
+region          container block -6 6 -6 6 -6 6 units box
+fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 48 every 566 steps, 100 by step 1133
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic/dof yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic/dof yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic/dof yes
+
+#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify	2 pad 5
+
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100          30   0.803783       0.803783       0.39507978     0.0029137134 
+       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
+       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
+       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
+       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
+       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
+       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
+       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
+      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
+      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
+      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
+      1400          99   0.35615284     0.35615284     0.19785725     0.0046170772 
+      1500          99   0.31486693     0.31486693     0.17429055     0.0064903432 
+      1600          99   0.26369001     0.26369001     0.15095266     0.0045226847 
+      1700         100   0.1925923      0.1925923      0.11308104     0.007362313  
+      1800         100   0.13724978     0.13724978     0.083276845    0.0058136373 
+      1900         100   0.077212636    0.077212636    0.053159386    0.0016509598 
+      2000         100   0.065294031    0.065294031    0.04372752     0.0020346467 
+      2100         100   0.057431398    0.057431398    0.037977068    0.0012681098 
+      2200         100   0.059093045    0.059093045    0.037435193    0.00096610799
+      2300         100   0.03422338     0.03422338     0.025491304    0.00069886052
+      2400         100   0.020558284    0.020558284    0.016163009    0.0017260663 
+      2500         100   0.015339709    0.015339709    0.012329236    0.00041308031
+      2600         100   0.012891354    0.012891354    0.009766054    0.00030356722
+      2700         100   0.0092634449   0.0092634449   0.0073580108   0.00077723051
+      2800         100   0.0073925841   0.0073925841   0.0059932218   0.00016466767
+      2900         100   0.0081228267   0.0081228267   0.006281761    0.00013828388
+      3000         100   0.0041833223   0.0041833223   0.0035147096   0.00013160599
+      3100         100   0.0035930775   0.0035930775   0.0030039922   0.00060639771
+      3200         100   0.0030824465   0.0030824465   0.0026541293   0.00047391014
+      3300         100   0.0035087522   0.0035087522   0.0027664508   0.00014080317
+      3400         100   0.0018537868   0.0018537868   0.0017099705   6.3326674e-05
+      3500         100   0.0015371228   0.0015371228   0.0014155433   0.00021612522
+      3600         100   0.001708556    0.001708556    0.0014369892   8.1034202e-05
+      3700         100   0.00095948652  0.00095948652  0.0009788528   3.4694023e-05
+      3800         100   0.00091875668  0.00091875668  0.00086805146  3.9373686e-05
+      3900         100   0.001557068    0.001557068    0.001159526    2.5178607e-05
+      4000         100   0.00062012451  0.00062012451  0.00066806922  5.6680551e-06
+      4100         100   0.00060940771  0.00060940771  0.00065614741  1.0137901e-05
+      4200         100   0.00059538437  0.00059538437  0.00064501521  7.3679744e-06
+      4300         100   0.00052946048  0.00052946048  0.00059353641  5.9225081e-06
+      4400         100   0.00051202281  0.00051202281  0.00057524772  3.6198435e-05
+      4500         100   0.00049986632  0.00049986632  0.00055754521  2.2275519e-05
+      4600         100   0.00048187334  0.00048187334  0.00053988815  2.2015243e-05
+      4700         100   0.00045261491  0.00045261491  0.00050298355  8.9681339e-05
+      4800         100   0.00034965427  0.00034965427  0.0004278781   1.0983535e-05
+      4900         100   0.00033555621  0.00033555621  0.00041435167  2.9266598e-05
+      5000         100   0.00031387148  0.00031387148  0.00039605781  2.5628425e-05
+Loop time of 0.078687 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 27450544.413 tau/day, 63542.927 timesteps/s, 6.354 Matom-step/s
+80.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0084151  | 0.0084151  | 0.0084151  |   0.0 | 10.69
+Neigh   | 0.012728   | 0.012728   | 0.012728   |   0.0 | 16.18
+Comm    | 0.0056143  | 0.0056143  | 0.0056143  |   0.0 |  7.14
+Output  | 0.00051411 | 0.00051411 | 0.00051411 |   0.0 |  0.65
+Modify  | 0.041412   | 0.041412   | 0.041412   |   0.0 | 52.63
+Other   |            | 0.01       |            |       | 12.71
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            164 ave         164 max         164 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 164
+Ave neighs/atom = 1.64
+Neighbor list builds = 281
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-5000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00031387148  0.00031387148  0.00039605781  2.6174978e-05
+      5100         100   0.54537023     0.54537023     0.30042175     0.0087427352 
+      5200         100   0.57210852     0.57210852     0.3192468      0.0098134067 
+      5300         100   0.7168108      0.7168108      0.38577893     0.011004584  
+      5400         100   0.78895524     0.78895524     0.41889428     0.013555713  
+      5500         100   0.87797874     0.87797874     0.45689223     0.01565356   
+      5600         100   0.95424379     0.95424379     0.48830429     0.014707858  
+      5700         100   1.0046012      1.0046012      0.51054927     0.01469179   
+      5800         100   1.0371453      1.0371453      0.5262568      0.015576788  
+      5900         100   1.0545743      1.0545743      0.5361173      0.01589889   
+      6000         100   1.0932949      1.0932949      0.55402214     0.017484573  
+      6100         100   1.1148364      1.1148364      0.56241126     0.01721788   
+      6200         100   1.1315267      1.1315267      0.57050887     0.017961246  
+      6300         100   1.1506124      1.1506124      0.58009471     0.017159062  
+      6400         100   1.1663328      1.1663328      0.5876586      0.017935311  
+      6500         100   1.1821086      1.1821086      0.59595162     0.018005316  
+      6600         100   1.2039397      1.2039397      0.60567524     0.021604669  
+      6700         100   1.2269911      1.2269911      0.61770224     0.018907995  
+      6800         100   1.2447035      1.2447035      0.6257652      0.02053766   
+      6900         100   1.2625323      1.2625323      0.63486698     0.020106134  
+      7000         100   1.2617127      1.2617127      0.63318163     0.019670429  
+      7100         100   1.260715       1.260715       0.63311254     0.019810631  
+      7200         100   1.2790404      1.2790404      0.64079001     0.020218903  
+      7300         100   1.2760228      1.2760228      0.6395331      0.021749906  
+      7400         100   1.2799658      1.2799658      0.64139084     0.020472922  
+      7500         100   1.2846473      1.2846473      0.64343085     0.020610025  
+      7600         100   1.2883965      1.2883965      0.64491873     0.02074884   
+      7700         100   1.2926891      1.2926891      0.64684545     0.020599654  
+      7800         100   1.3032201      1.3032201      0.65119455     0.02183405   
+      7900         100   1.3025628      1.3025628      0.65068661     0.021248589  
+      8000         100   1.3052302      1.3052302      0.65208602     0.021399549  
+      8100         100   1.3069867      1.3069867      0.65304849     0.021254794  
+      8200         100   1.3092024      1.3092024      0.6543837      0.021220909  
+      8300         100   1.3101468      1.3101468      0.65519741     0.021328361  
+      8400         100   1.3116005      1.3116005      0.65545253     0.021493555  
+      8500         100   1.3153616      1.3153616      0.65731542     0.021433279  
+      8600         100   1.3164556      1.3164556      0.65791227     0.021531213  
+      8700         100   1.3187245      1.3187245      0.65915974     0.02170181   
+      8800         100   1.3215981      1.3215981      0.66036644     0.022358849  
+      8900         100   1.3206845      1.3206845      0.65984651     0.021901337  
+      9000         100   1.3213046      1.3213046      0.66020378     0.021876353  
+      9100         100   1.3225084      1.3225084      0.66088847     0.021811098  
+      9200         100   1.3240309      1.3240309      0.66180646     0.021768929  
+      9300         100   1.325458       1.325458       0.66280401     0.02165852   
+      9400         100   1.3322968      1.3322968      0.66615126     0.022139018  
+      9500         100   1.3416035      1.3416035      0.67030794     0.022243129  
+      9600         100   1.3353326      1.3353326      0.66692811     0.022622122  
+      9700         100   1.336265       1.336265       0.66727395     0.022171165  
+      9800         100   1.3344531      1.3344531      0.66634538     0.022025131  
+      9900         100   1.3337098      1.3337098      0.66601721     0.022111706  
+     10000         100   1.3335539      1.3335539      0.66597627     0.022133817  
+Loop time of 0.235008 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 9191156.994 tau/day, 21275.826 timesteps/s, 2.128 Matom-step/s
+94.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.029846   | 0.029846   | 0.029846   |   0.0 | 12.70
+Neigh   | 0.030211   | 0.030211   | 0.030211   |   0.0 | 12.86
+Comm    | 0.005731   | 0.005731   | 0.005731   |   0.0 |  2.44
+Output  | 0.00051873 | 0.00051873 | 0.00051873 |   0.0 |  0.22
+Modify  | 0.1583     | 0.1583     | 0.1583     |   0.0 | 67.36
+Other   |            | 0.01041    |            |       |  4.43
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            186 ave         186 max         186 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 186
+Ave neighs/atom = 1.86
+Neighbor list builds = 626
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   1.3335539      1.3335539      0.66597627     0.022207076  
+     10100         100   0.29976134     0.29976134     0.1752962      0.0091355801 
+     10200         100   0.1548002      0.1548002      0.1005356      0.0062509071 
+     10300         100   0.082468613    0.082468613    0.066729575    0.0017315098 
+     10400         100   0.06731284     0.06731284     0.056685383    0.0011965765 
+     10500         100   0.050167538    0.050167538    0.042388389    0.0010830279 
+     10600         100   0.041091371    0.041091371    0.034743534    0.00092984522
+     10700         100   0.033199041    0.033199041    0.027954031    0.0018451338 
+     10800         100   0.027880411    0.027880411    0.024437224    0.0013039536 
+     10900         100   0.024634597    0.024634597    0.021815184    0.00030935286
+     11000         100   0.020741105    0.020741105    0.018754221    0.0006306901 
+     11100         100   0.017210914    0.017210914    0.015842306    0.00075930229
+     11200         100   0.01254319     0.01254319     0.012145795    0.00047388541
+     11300         100   0.010032468    0.010032468    0.0095918697   0.0014677116 
+     11400         100   0.0081538458   0.0081538458   0.0080985914   0.00032485316
+     11500         100   0.0072918155   0.0072918155   0.0070156789   0.00023642827
+     11600         100   0.0070136586   0.0070136586   0.0067263114   7.8490444e-05
+     11700         100   0.0061722946   0.0061722946   0.0058832419   0.00013450793
+     11800         100   0.0052444487   0.0052444487   0.0049294304   8.6973121e-05
+     11900         100   0.0048212279   0.0048212279   0.0045261412   0.00010458031
+     12000         100   0.0046782797   0.0046782797   0.0044011937   0.00018881094
+     12100         100   0.0042066617   0.0042066617   0.0040330976   0.00015507521
+     12200         100   0.0038529032   0.0038529032   0.003664712    1.1476621e-05
+     12300         100   0.0033203238   0.0033203238   0.0032404054   0.00027622191
+     12400         100   0.003113731    0.003113731    0.0030491123   3.8532421e-05
+     12500         100   0.0029925149   0.0029925149   0.0029415075   4.2673261e-05
+     12600         100   0.0028383323   0.0028383323   0.0027902992   9.328552e-05 
+     12700         100   0.0026386104   0.0026386104   0.0026095714   7.7740986e-05
+     12800         100   0.0023509873   0.0023509873   0.0023518594   3.1944764e-05
+     12900         100   0.0022296104   0.0022296104   0.0022030693   4.5393502e-05
+     13000         100   0.0021991358   0.0021991358   0.0021560478   0.0001221212 
+     13100         100   0.0021011001   0.0021011001   0.0020752855   2.4605107e-05
+     13200         100   0.002004495    0.002004495    0.0020040212   2.4805625e-05
+     13300         100   0.0018394135   0.0018394135   0.0018288384   6.2227066e-05
+     13400         100   0.0016314086   0.0016314086   0.0016058102   0.00010372886
+     13500         100   0.0015042857   0.0015042857   0.0014660263   0.00020805178
+     13600         100   0.0013584764   0.0013584764   0.0013177418   5.1603333e-05
+     13700         100   0.0012407449   0.0012407449   0.0011902637   8.87401e-05  
+     13800         100   0.0011673364   0.0011673364   0.0011324247   2.3668551e-05
+     13900         100   0.0011429204   0.0011429204   0.0011072347   1.414364e-05 
+     14000         100   0.001087543    0.001087543    0.0010616439   3.0874865e-05
+     14100         100   0.00098839393  0.00098839393  0.00096445684  6.5331515e-05
+     14200         100   0.00095139076  0.00095139076  0.00093658993  2.5649208e-05
+     14300         100   0.00089532494  0.00089532494  0.00082626435  2.6200482e-05
+     14400         100   0.00077973015  0.00077973015  0.00070733785  2.29298e-05  
+     14500         100   0.00068559117  0.00068559117  0.00062297009  8.4841907e-06
+     14600         100   0.00059199698  0.00059199698  0.00052453148  1.2737231e-05
+     14700         100   0.00055052378  0.00055052378  0.00048459372  1.3028328e-05
+     14800         100   0.00049397913  0.00049397913  0.00044094284  6.1129918e-06
+     14900         100   0.00048082746  0.00048082746  0.00043128724  3.7301936e-06
+     15000         100   0.00046847825  0.00046847825  0.00041484245  5.7974184e-06
+Loop time of 0.0802044 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 26931180.398 tau/day, 62340.695 timesteps/s, 6.234 Matom-step/s
+82.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0080809  | 0.0080809  | 0.0080809  |   0.0 | 10.08
+Neigh   | 0.0048815  | 0.0048815  | 0.0048815  |   0.0 |  6.09
+Comm    | 0.0055605  | 0.0055605  | 0.0055605  |   0.0 |  6.93
+Output  | 0.00050386 | 0.00050386 | 0.00050386 |   0.0 |  0.63
+Modify  | 0.051104   | 0.051104   | 0.051104   |   0.0 | 63.72
+Other   |            | 0.01007    |            |       | 12.56
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            157 ave         157 max         157 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 157
+Ave neighs/atom = 1.57
+Neighbor list builds = 100
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-15000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00046847825  0.00046847825  0.00041484245  5.7974184e-06
+     15100         100   0.96677694     0.96677694     0.64420785     0.01431184   
+     15200         100   1.0659255      1.0659255      0.69293741     0.013240486  
+     15300         100   1.1647631      1.1647631      0.75191941     0.014622673  
+     15400         100   1.3411593      1.3411593      0.85696383     0.02561549   
+     15500         100   1.6033758      1.6033758      0.99094919     0.026221789  
+     15600         100   1.7889645      1.7889645      1.075315       0.024116301  
+     15700         100   1.8077023      1.8077023      1.0842652      0.031781756  
+     15800         100   2.0252655      2.0252655      1.1517407      0.037201818  
+     15900         100   2.1479427      2.1479427      1.2061238      0.027668435  
+     16000         100   2.1788838      2.1788838      1.2205599      0.029114273  
+     16100         100   2.3257431      2.3257431      1.2921157      0.035663063  
+     16200         100   2.3885449      2.3885449      1.3282237      0.032255517  
+     16300         100   2.3670966      2.3670966      1.3091694      0.029579008  
+     16400         100   2.5097781      2.5097781      1.3712036      0.034579196  
+     16500         100   2.6440883      2.6440883      1.4440043      0.03347813   
+     16600         100   2.7230084      2.7230084      1.481565       0.036660339  
+     16700         100   2.8246108      2.8246108      1.5298387      0.035623641  
+     16800         100   3.0338694      3.0338694      1.6333504      0.038818594  
+     16900         100   3.1219584      3.1219584      1.6790766      0.043444123  
+     17000         100   3.4103817      3.4103817      1.8222668      0.044524654  
+     17100         100   3.3869069      3.3869069      1.8170743      0.050670801  
+     17200         100   3.4220314      3.4220314      1.8312364      0.045956123  
+     17300         100   3.396894       3.396894       1.8158291      0.050420297  
+     17400         100   3.4508224      3.4508224      1.8429996      0.049923733  
+     17500         100   3.5039601      3.5039601      1.8822352      0.051047713  
+     17600         100   3.3743905      3.3743905      1.8380347      0.047922214  
+     17700         100   3.3729709      3.3729709      1.8224123      0.04758126   
+     17800         100   3.3237798      3.3237798      1.7962316      0.045427975  
+     17900         100   3.2441052      3.2441052      1.7782748      0.044651231  
+     18000         100   3.1169205      3.1169205      1.704639       0.047440495  
+     18100         100   3.1704608      3.1704608      1.7326375      0.045656546  
+     18200         100   3.1113438      3.1113438      1.7002232      0.041619255  
+     18300         100   3.2506111      3.2506111      1.7693075      0.048028527  
+     18400         100   3.3840681      3.3840681      1.8370672      0.04443243   
+     18500         100   3.4822823      3.4822823      1.9125273      0.043687118  
+     18600         100   3.5214372      3.5214372      1.9364829      0.049798605  
+     18700         100   3.5439229      3.5439229      1.9441301      0.046240266  
+     18800         100   3.6046761      3.6046761      1.9791448      0.054369382  
+     18900         100   3.8598403      3.8598403      2.0999449      0.049863074  
+     19000         100   3.8606461      3.8606461      2.0885493      0.050269245  
+     19100         100   4.076627       4.076627       2.2025766      0.058050893  
+     19200         100   3.8280814      3.8280814      2.0749884      0.05730905   
+     19300         100   3.8211633      3.8211633      2.0759453      0.05145071   
+     19400         100   3.7726284      3.7726284      2.0466555      0.053566404  
+     19500         100   3.7468403      3.7468403      2.03218        0.048422025  
+     19600         100   3.6408955      3.6408955      1.9873843      0.046565134  
+     19700         100   3.6454187      3.6454187      2.0042204      0.049299897  
+     19800         100   3.5165071      3.5165071      1.937379       0.046319859  
+     19900         100   3.4670702      3.4670702      1.9140316      0.045650114  
+     20000         100   3.6114294      3.6114294      1.9798674      0.05431148   
+Loop time of 0.203164 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 10631806.993 tau/day, 24610.664 timesteps/s, 2.461 Matom-step/s
+92.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.01242    | 0.01242    | 0.01242    |   0.0 |  6.11
+Neigh   | 0.044478   | 0.044478   | 0.044478   |   0.0 | 21.89
+Comm    | 0.0057766  | 0.0057766  | 0.0057766  |   0.0 |  2.84
+Output  | 0.00051702 | 0.00051702 | 0.00051702 |   0.0 |  0.25
+Modify  | 0.12923    | 0.12923    | 0.12923    |   0.0 | 63.61
+Other   |            | 0.01074    |            |       |  5.29
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            142 ave         142 max         142 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 142
+Ave neighs/atom = 1.42
+Neighbor list builds = 909
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   3.6114294      3.6114294      1.9798674      0.053887263  
+     20100         100   1.0907336      1.0907336      0.69799767     0.013925984  
+     20200         100   0.92304387     0.92304387     0.59520318     0.012377709  
+     20300         100   0.84004201     0.84004201     0.55081472     0.012108246  
+     20400         100   0.89491209     0.89491209     0.56269969     0.01221427   
+     20500         100   0.92011482     0.92011482     0.56971815     0.011353588  
+     20600         100   0.95722998     0.95722998     0.58038747     0.01185569   
+     20700         100   0.92635786     0.92635786     0.55373959     0.011953734  
+     20800         100   0.93088162     0.93088162     0.55094813     0.012887472  
+     20900         100   0.97288373     0.97288373     0.56309599     0.013731021  
+     21000         100   0.63378762     0.63378762     0.3779177      0.010114787  
+     21100         100   0.34618473     0.34618473     0.21652381     0.0070717708 
+     21200         100   0.18660008     0.18660008     0.1302051      0.006504227  
+     21300         100   0.13917709     0.13917709     0.09667499     0.0032593765 
+     21400         100   0.11627047     0.11627047     0.080272858    0.0028891045 
+     21500         100   0.086269781    0.086269781    0.064184981    0.0019374959 
+     21600         100   0.08052393     0.08052393     0.059561101    0.001214522  
+     21700         100   0.036026032    0.036026032    0.030243348    0.001199233  
+     21800         100   0.02392645     0.02392645     0.022284244    0.00060060634
+     21900         100   0.016991266    0.016991266    0.017366625    0.00065672411
+     22000         100   0.016974877    0.016974877    0.016399245    0.0005903103 
+     22100         100   0.015491818    0.015491818    0.014806105    0.00051181051
+     22200         100   0.011908698    0.011908698    0.011206673    0.00099478656
+     22300         100   0.010002714    0.010002714    0.0093749794   0.00028214624
+     22400         100   0.0081652616   0.0081652616   0.0079594664   0.00026841276
+     22500         100   0.0067602843   0.0067602843   0.0067498831   0.00019472612
+     22600         100   0.0061024058   0.0061024058   0.0062958451   0.00016615781
+     22700         100   0.005331422    0.005331422    0.0056152366   0.00021543475
+     22800         100   0.0040796708   0.0040796708   0.004140932    0.00024397062
+     22900         100   0.0042042089   0.0042042089   0.0040406804   0.00015880055
+     23000         100   0.0056083872   0.0056083872   0.0046056699   0.00029203396
+     23100         100   0.0035006398   0.0035006398   0.003343101    0.00010571574
+     23200         100   0.0032402473   0.0032402473   0.003122476    0.00012784403
+     23300         100   0.0030100724   0.0030100724   0.0029649423   8.5613724e-05
+     23400         100   0.002746305    0.002746305    0.0027519317   9.6521844e-05
+     23500         100   0.0028543876   0.0028543876   0.002842845    0.00012566665
+     23600         100   0.0036979234   0.0036979234   0.0032448309   8.6321879e-05
+     23700         100   0.0030503565   0.0030503565   0.0027392305   5.9716835e-05
+     23800         100   0.0021564041   0.0021564041   0.0022097768   0.00028317769
+     23900         100   0.0018905956   0.0018905956   0.0020002233   4.5205733e-05
+     24000         100   0.0015705513   0.0015705513   0.0017262538   0.00026550225
+     24100         100   0.0013341334   0.0013341334   0.0015663921   4.8307183e-05
+     24200         100   0.0012426828   0.0012426828   0.0014960127   5.5195907e-05
+     24300         100   0.0011933799   0.0011933799   0.0014508697   5.2781568e-05
+     24400         100   0.0010126015   0.0010126015   0.0012821281   0.00011096457
+     24500         100   0.00094102576  0.00094102576  0.0012265703   3.3454252e-05
+     24600         100   0.00092243997  0.00092243997  0.0011970533   3.7288789e-05
+     24700         100   0.00080565605  0.00080565605  0.0010864406   0.00015797228
+     24800         100   0.00075303124  0.00075303124  0.0010103671   5.4727635e-05
+     24900         100   0.00074808599  0.00074808599  0.0010053951   8.6607732e-05
+     25000         100   0.00071720457  0.00071720457  0.00096622937  0.00015861964
+Loop time of 0.0845534 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 25545994.179 tau/day, 59134.246 timesteps/s, 5.913 Matom-step/s
+90.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0091411  | 0.0091411  | 0.0091411  |   0.0 | 10.81
+Neigh   | 0.013557   | 0.013557   | 0.013557   |   0.0 | 16.03
+Comm    | 0.0056205  | 0.0056205  | 0.0056205  |   0.0 |  6.65
+Output  | 0.0005087  | 0.0005087  | 0.0005087  |   0.0 |  0.60
+Modify  | 0.045578   | 0.045578   | 0.045578   |   0.0 | 53.90
+Other   |            | 0.01015    |            |       | 12.00
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            151 ave         151 max         151 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 151
+Ave neighs/atom = 1.51
+Neighbor list builds = 286
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/granregion/log.15Sep22.granregion.box.g++.4

@@ -0,0 +1,493 @@
+LAMMPS (15 Sep 2022)
+# pouring spheres into container box
+
+units		lj
+atom_style      sphere
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -10 10 -10 10 -10 10 units box
+create_box      2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* * gran/hooke
+
+region          container block -6 6 -6 6 -6 6 units box
+fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 48 every 566 steps, 100 by step 1133
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic/dof yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic/dof yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic/dof yes
+
+#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify	2 pad 5
+
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100          30   0.803783       0.803783       0.39507978     0.0029137134 
+       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
+       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
+       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
+       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
+       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
+       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
+       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
+      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
+      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
+      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
+      1400          99   0.35615284     0.35615284     0.19785725     0.0046170774 
+      1500          99   0.31486691     0.31486691     0.17429054     0.0064903404 
+      1600          99   0.26369        0.26369        0.15095263     0.0045226821 
+      1700         100   0.19259352     0.19259352     0.11308184     0.0073603886 
+      1800         100   0.1372448      0.1372448      0.083273652    0.0058163062 
+      1900         100   0.077253038    0.077253038    0.053166156    0.0017440856 
+      2000         100   0.065472093    0.065472093    0.04375349     0.0018416047 
+      2100         100   0.057213469    0.057213469    0.037773954    0.001226231  
+      2200         100   0.058857437    0.058857437    0.0372655      0.00090812381
+      2300         100   0.035066108    0.035066108    0.025934054    0.00072114554
+      2400         100   0.021272125    0.021272125    0.016635107    0.0018506654 
+      2500         100   0.015530432    0.015530432    0.012533546    0.0013883971 
+      2600         100   0.012603946    0.012603946    0.0096981459   0.00038648118
+      2700         100   0.0097347475   0.0097347475   0.0076016624   0.00057313888
+      2800         100   0.0067081771   0.0067081771   0.0056944431   0.00085080075
+      2900         100   0.0089177981   0.0089177981   0.0065036822   0.00028986539
+      3000         100   0.0057840287   0.0057840287   0.0044989265   0.00016111737
+      3100         100   0.0038909621   0.0038909621   0.0031511938   0.0001708892 
+      3200         100   0.0029043214   0.0029043214   0.0025807767   9.2473673e-05
+      3300         100   0.0022769336   0.0022769336   0.0021487157   0.00022312666
+      3400         100   0.0015571397   0.0015571397   0.0016669068   0.0003381372 
+      3500         100   0.0015978184   0.0015978184   0.001707772    4.9930818e-05
+      3600         100   0.0023358916   0.0023358916   0.0020709426   9.7687609e-05
+      3700         100   0.0011186736   0.0011186736   0.0012146914   9.3338234e-05
+      3800         100   0.0011657036   0.0011657036   0.0012313764   3.1931251e-05
+      3900         100   0.0014998387   0.0014998387   0.0014015491   2.4226798e-05
+      4000         100   0.0010858335   0.0010858335   0.0010623286   1.6359241e-05
+      4100         100   0.0010464314   0.0010464314   0.0010123557   1.2949588e-05
+      4200         100   0.0010022428   0.0010022428   0.00097338971  1.2402332e-05
+      4300         100   0.00080622372  0.00080622372  0.00084329652  0.00033857037
+      4400         100   0.00073613921  0.00073613921  0.00078373608  1.0103949e-05
+      4500         100   0.00071402196  0.00071402196  0.00076658004  8.8360218e-06
+      4600         100   0.00064851765  0.00064851765  0.00071533461  1.0736438e-05
+      4700         100   0.00061146699  0.00061146699  0.00068274687  4.1341755e-06
+      4800         100   0.00059511472  0.00059511472  0.0006625527   7.3645447e-06
+      4900         100   0.00057700347  0.00057700347  0.0006468562   1.5411897e-05
+      5000         100   0.00056205001  0.00056205001  0.00063592505  7.8813845e-06
+Loop time of 0.0856033 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 25232672.400 tau/day, 58408.964 timesteps/s, 5.841 Matom-step/s
+88.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0034695  | 0.0050634  | 0.0068805  |   2.2 |  5.91
+Neigh   | 0.0016916  | 0.0024175  | 0.0032212  |   1.5 |  2.82
+Comm    | 0.020003   | 0.026482   | 0.033796   |   3.5 | 30.94
+Output  | 0.0010864  | 0.001327   | 0.0014374  |   0.4 |  1.55
+Modify  | 0.0067352  | 0.015857   | 0.025751   |   7.2 | 18.52
+Other   |            | 0.03446    |            |       | 40.25
+
+Nlocal:             25 ave          53 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:              4 ave           8 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           40.5 ave          92 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 162
+Ave neighs/atom = 1.62
+Neighbor list builds = 288
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-5000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.734 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00056205001  0.00056205001  0.00063592505  7.871665e-06 
+      5100         100   0.59585977     0.59585977     0.32464933     0.0141718    
+      5200         100   0.67306764     0.67306764     0.35872096     0.013373672  
+      5300         100   0.76065187     0.76065187     0.39925025     0.011460301  
+      5400         100   0.87984446     0.87984446     0.45261417     0.013937042  
+      5500         100   0.95548319     0.95548319     0.48706892     0.013601658  
+      5600         100   0.9993278      0.9993278      0.50830306     0.015663766  
+      5700         100   1.0449415      1.0449415      0.52967249     0.016797841  
+      5800         100   1.0767598      1.0767598      0.54508699     0.016128855  
+      5900         100   1.118688       1.118688       0.56530849     0.016830117  
+      6000         100   1.1535698      1.1535698      0.58290663     0.01715335   
+      6100         100   1.1753828      1.1753828      0.59419088     0.019273207  
+      6200         100   1.1994171      1.1994171      0.60433264     0.018391566  
+      6300         100   1.2244707      1.2244707      0.61626199     0.018842556  
+      6400         100   1.2507994      1.2507994      0.62829386     0.019538413  
+      6500         100   1.2684644      1.2684644      0.63747702     0.020794729  
+      6600         100   1.2704726      1.2704726      0.63929889     0.020253985  
+      6700         100   1.2737302      1.2737302      0.63970688     0.020858602  
+      6800         100   1.287922       1.287922       0.64460894     0.021589773  
+      6900         100   1.3028782      1.3028782      0.65197802     0.02135295   
+      7000         100   1.306633       1.306633       0.65371741     0.021291182  
+      7100         100   1.3161393      1.3161393      0.65785404     0.022554896  
+      7200         100   1.3228158      1.3228158      0.6609031      0.021811977  
+      7300         100   1.3245632      1.3245632      0.66161966     0.02206776   
+      7400         100   1.3266822      1.3266822      0.662738       0.022070761  
+      7500         100   1.3265138      1.3265138      0.6624472      0.021944768  
+      7600         100   1.3286802      1.3286802      0.66338775     0.0219393    
+      7700         100   1.332829       1.332829       0.66547051     0.022142398  
+      7800         100   1.3323535      1.3323535      0.66534513     0.022787777  
+      7900         100   1.3372424      1.3372424      0.66777556     0.02192759   
+      8000         100   1.3396201      1.3396201      0.66910123     0.022439596  
+      8100         100   1.3422271      1.3422271      0.67060566     0.023784952  
+      8200         100   1.3468062      1.3468062      0.6728991      0.02243345   
+      8300         100   1.3439408      1.3439408      0.6717529      0.022312339  
+      8400         100   1.3484134      1.3484134      0.67346027     0.022770922  
+      8500         100   1.3490032      1.3490032      0.67378177     0.022427863  
+      8600         100   1.349789       1.349789       0.67398897     0.022494049  
+      8700         100   1.3513512      1.3513512      0.67475613     0.022413559  
+      8800         100   1.3535168      1.3535168      0.67589784     0.022356566  
+      8900         100   1.3505765      1.3505765      0.67442168     0.022240615  
+      9000         100   1.3499918      1.3499918      0.67419831     0.02226049   
+      9100         100   1.3518103      1.3518103      0.67489482     0.022399038  
+      9200         100   1.3526275      1.3526275      0.67529852     0.022395079  
+      9300         100   1.353741       1.353741       0.67585205     0.022471008  
+      9400         100   1.3538758      1.3538758      0.67589523     0.022461734  
+      9500         100   1.3537199      1.3537199      0.67586527     0.022370169  
+      9600         100   1.3539788      1.3539788      0.67602899     0.022400771  
+      9700         100   1.3544874      1.3544874      0.67619552     0.022648464  
+      9800         100   1.3555422      1.3555422      0.67666186     0.022367319  
+      9900         100   1.3560106      1.3560106      0.6768751      0.02236585   
+     10000         100   1.3563578      1.3563578      0.6770434      0.022359307  
+Loop time of 0.139615 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 15471121.710 tau/day, 35812.782 timesteps/s, 3.581 Matom-step/s
+89.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0034672  | 0.011349   | 0.019511   |   7.2 |  8.13
+Neigh   | 0.0032972  | 0.0053674  | 0.0074946  |   2.8 |  3.84
+Comm    | 0.011049   | 0.018572   | 0.027876   |   5.6 | 13.30
+Output  | 0.0010807  | 0.0015593  | 0.0018738  |   0.8 |  1.12
+Modify  | 0.013556   | 0.040435   | 0.066715   |  13.0 | 28.96
+Other   |            | 0.06233    |            |       | 44.65
+
+Nlocal:             25 ave          52 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:              3 ave           6 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:          48.25 ave         109 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 193
+Ave neighs/atom = 1.93
+Neighbor list builds = 626
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   1.3563578      1.3563578      0.6770434      0.022433108  
+     10100         100   0.32881547     0.32881547     0.18968913     0.0063460187 
+     10200         100   0.19880113     0.19880113     0.12812646     0.0074601538 
+     10300         100   0.12614062     0.12614062     0.090121373    0.0028337336 
+     10400         100   0.088358363    0.088358363    0.067236815    0.0020269846 
+     10500         100   0.071199344    0.071199344    0.055567135    0.0016191769 
+     10600         100   0.053909616    0.053909616    0.042301996    0.00098643468
+     10700         100   0.039560745    0.039560745    0.032482256    0.00089240864
+     10800         100   0.032130432    0.032130432    0.02705329     0.00058669881
+     10900         100   0.02462494     0.02462494     0.021121496    0.0017376127 
+     11000         100   0.020941068    0.020941068    0.017866781    0.00031112553
+     11100         100   0.016775675    0.016775675    0.014620214    0.00026856842
+     11200         100   0.015005732    0.015005732    0.012803923    0.00067036626
+     11300         100   0.012099209    0.012099209    0.010308221    0.00032666902
+     11400         100   0.010559421    0.010559421    0.0090243729   0.00013645685
+     11500         100   0.0093738615   0.0093738615   0.0080176514   0.00098541099
+     11600         100   0.0081900702   0.0081900702   0.0070256953   0.00025935992
+     11700         100   0.0068100165   0.0068100165   0.0058703223   0.00014866816
+     11800         100   0.0060475708   0.0060475708   0.0052518105   0.00017895168
+     11900         100   0.0055607485   0.0055607485   0.0047184164   0.00011358846
+     12000         100   0.0053149064   0.0053149064   0.0045168418   0.00015222428
+     12100         100   0.0050909525   0.0050909525   0.0043196952   6.3000537e-05
+     12200         100   0.0041810842   0.0041810842   0.0036835522   4.6423956e-05
+     12300         100   0.0034305227   0.0034305227   0.0031222649   0.00020251115
+     12400         100   0.0031763077   0.0031763077   0.0028956456   0.00030307787
+     12500         100   0.0027440829   0.0027440829   0.0025087304   0.00010418607
+     12600         100   0.0024581964   0.0024581964   0.0022200229   3.042018e-05 
+     12700         100   0.002259527    0.002259527    0.0020708869   4.192368e-05 
+     12800         100   0.0019143448   0.0019143448   0.0018088032   4.6200439e-05
+     12900         100   0.0017935964   0.0017935964   0.0017028317   2.2195756e-05
+     13000         100   0.0017286429   0.0017286429   0.0016396753   2.3108871e-05
+     13100         100   0.0017055291   0.0017055291   0.0016122058   2.2444611e-05
+     13200         100   0.0016539275   0.0016539275   0.0015570166   2.0467353e-05
+     13300         100   0.0015777788   0.0015777788   0.0014852505   1.9525012e-05
+     13400         100   0.0015372199   0.0015372199   0.0014497102   2.3203566e-05
+     13500         100   0.0015066638   0.0015066638   0.0014097203   1.8644964e-05
+     13600         100   0.0012290618   0.0012290618   0.0012056216   1.3235643e-05
+     13700         100   0.0011781948   0.0011781948   0.0011685226   3.4312262e-05
+     13800         100   0.0011530136   0.0011530136   0.0011433171   2.8832126e-05
+     13900         100   0.0011085224   0.0011085224   0.0011052764   1.444139e-05 
+     14000         100   0.0010656788   0.0010656788   0.0010702461   1.3187775e-05
+     14100         100   0.001029277    0.001029277    0.0010469537   1.2837267e-05
+     14200         100   0.0009750904   0.0009750904   0.0009915384   1.209089e-05 
+     14300         100   0.00094893337  0.00094893337  0.00096909301  1.1743051e-05
+     14400         100   0.00087708427  0.00087708427  0.00087575318  1.9027338e-05
+     14500         100   0.00086229913  0.00086229913  0.0008643568   1.0670952e-05
+     14600         100   0.00084206808  0.00084206808  0.0008268172   3.2391722e-05
+     14700         100   0.00077682873  0.00077682873  0.00077186085  9.6132555e-06
+     14800         100   0.00074736908  0.00074736908  0.00074958372  9.2486924e-06
+     14900         100   0.00074456847  0.00074456847  0.00074779946  9.2140349e-06
+     15000         100   0.00073830282  0.00073830282  0.0007426924   9.1364974e-06
+Loop time of 0.0808149 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 26727738.394 tau/day, 61869.765 timesteps/s, 6.187 Matom-step/s
+86.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0034354  | 0.0050332  | 0.0069329  |   2.2 |  6.23
+Neigh   | 0.00051999 | 0.00084906 | 0.0012075  |   0.0 |  1.05
+Comm    | 0.0063631  | 0.014527   | 0.023754   |   6.8 | 17.98
+Output  | 0.0010373  | 0.001342   | 0.001464   |   0.5 |  1.66
+Modify  | 0.0051837  | 0.017338   | 0.031605   |   9.3 | 21.45
+Other   |            | 0.04173    |            |       | 51.63
+
+Nlocal:             25 ave          53 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:           3.75 ave           8 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:          39.25 ave          82 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 157
+Ave neighs/atom = 1.57
+Neighbor list builds = 100
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-15000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00073830282  0.00073830282  0.0007426924   9.1364974e-06
+     15100         100   1.1048281      1.1048281      0.7023727      0.018379275  
+     15200         100   1.2022249      1.2022249      0.77748962     0.015662439  
+     15300         100   1.2561351      1.2561351      0.82563065     0.01835048   
+     15400         100   1.4372446      1.4372446      0.92907923     0.02087065   
+     15500         100   1.6414713      1.6414713      1.0284489      0.025654324  
+     15600         100   1.7844655      1.7844655      1.0861866      0.025170346  
+     15700         100   2.034248       2.034248       1.2017171      0.040341642  
+     15800         100   2.1253699      2.1253699      1.2228657      0.029297194  
+     15900         100   2.1940232      2.1940232      1.2470589      0.033866758  
+     16000         100   2.2624419      2.2624419      1.2828225      0.030063645  
+     16100         100   2.3208536      2.3208536      1.3118956      0.0323489    
+     16200         100   2.3564971      2.3564971      1.3261173      0.032882494  
+     16300         100   2.3956066      2.3956066      1.3260307      0.03292972   
+     16400         100   2.5025831      2.5025831      1.3817693      0.031132988  
+     16500         100   2.5947914      2.5947914      1.4152657      0.036126782  
+     16600         100   2.7688769      2.7688769      1.4975686      0.037497127  
+     16700         100   2.812503       2.812503       1.5216659      0.039316167  
+     16800         100   2.8977424      2.8977424      1.5599254      0.039996029  
+     16900         100   3.045802       3.045802       1.6332888      0.041406156  
+     17000         100   3.2195366      3.2195366      1.7247171      0.040023634  
+     17100         100   3.2597294      3.2597294      1.7527958      0.04828292   
+     17200         100   3.293587       3.293587       1.7693254      0.044001441  
+     17300         100   3.1861836      3.1861836      1.7142076      0.049158822  
+     17400         100   3.4593561      3.4593561      1.8426619      0.053469673  
+     17500         100   3.3813767      3.3813767      1.8079958      0.058776299  
+     17600         100   3.5834203      3.5834203      1.9094759      0.053256842  
+     17700         100   3.2243306      3.2243306      1.7425111      0.064354789  
+     17800         100   3.358228       3.358228       1.8202932      0.046798524  
+     17900         100   3.2257908      3.2257908      1.7678964      0.043655204  
+     18000         100   3.237732       3.237732       1.7598181      0.050850672  
+     18100         100   3.2042441      3.2042441      1.751979       0.045582006  
+     18200         100   3.1562775      3.1562775      1.7336068      0.042210739  
+     18300         100   3.2630507      3.2630507      1.7925333      0.046412778  
+     18400         100   3.4150588      3.4150588      1.8668408      0.044386435  
+     18500         100   3.4913198      3.4913198      1.9125495      0.043329829  
+     18600         100   3.5290036      3.5290036      1.9184098      0.048302721  
+     18700         100   3.4852698      3.4852698      1.8865833      0.059566124  
+     18800         100   3.7157551      3.7157551      2.0082235      0.051356305  
+     18900         100   3.9504619      3.9504619      2.1377018      0.051553987  
+     19000         100   3.9711274      3.9711274      2.1549121      0.051555312  
+     19100         100   3.90954        3.90954        2.1135174      0.0548311    
+     19200         100   4.0672819      4.0672819      2.1837089      0.064431553  
+     19300         100   3.998355       3.998355       2.1572884      0.056830399  
+     19400         100   3.9172127      3.9172127      2.1130164      0.051264041  
+     19500         100   3.9120291      3.9120291      2.1088399      0.052545115  
+     19600         100   3.8613614      3.8613614      2.0752883      0.055466569  
+     19700         100   3.8428824      3.8428824      2.0787804      0.05129261   
+     19800         100   3.5686751      3.5686751      1.9356553      0.059177256  
+     19900         100   3.5573788      3.5573788      1.9430183      0.054618794  
+     20000         100   3.5453022      3.5453022      1.9413343      0.047640543  
+Loop time of 0.13841 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 15605800.739 tau/day, 36124.539 timesteps/s, 3.612 Matom-step/s
+89.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0047469  | 0.0062771  | 0.0080644  |   1.5 |  4.54
+Neigh   | 0.0062517  | 0.0079248  | 0.0094271  |   1.3 |  5.73
+Comm    | 0.047109   | 0.048595   | 0.050543   |   0.6 | 35.11
+Output  | 0.0011807  | 0.0013428  | 0.0015517  |   0.4 |  0.97
+Modify  | 0.022766   | 0.033256   | 0.039993   |   3.5 | 24.03
+Other   |            | 0.04101    |            |       | 29.63
+
+Nlocal:             25 ave          36 max          13 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost:              5 ave           9 max           2 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:           37.5 ave          53 max          15 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 150
+Ave neighs/atom = 1.5
+Neighbor list builds = 913
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   3.5453022      3.5453022      1.9413343      0.047178052  
+     20100         100   1.0878587      1.0878587      0.68666704     0.016139979  
+     20200         100   1.0230655      1.0230655      0.63593494     0.014642345  
+     20300         100   0.94958824     0.94958824     0.59306601     0.011745659  
+     20400         100   0.93038108     0.93038108     0.57232527     0.01154829   
+     20500         100   0.92183816     0.92183816     0.55466942     0.01212559   
+     20600         100   1.0175846      1.0175846      0.59940035     0.013815361  
+     20700         100   1.0564615      1.0564615      0.60726745     0.013073711  
+     20800         100   0.99967869     0.99967869     0.57665019     0.012450813  
+     20900         100   0.97051084     0.97051084     0.5574217      0.015686955  
+     21000         100   0.639185       0.639185       0.37441942     0.017594616  
+     21100         100   0.24979014     0.24979014     0.17121567     0.0084027295 
+     21200         100   0.15147941     0.15147941     0.11124349     0.0030435746 
+     21300         100   0.13117502     0.13117502     0.091432638    0.0029110318 
+     21400         100   0.11158272     0.11158272     0.076264692    0.0021951204 
+     21500         100   0.056660993    0.056660993    0.043503807    0.0010993096 
+     21600         100   0.028640836    0.028640836    0.026000267    0.0010440792 
+     21700         100   0.025816483    0.025816483    0.021922896    0.00081674646
+     21800         100   0.023929555    0.023929555    0.019936972    0.0010383614 
+     21900         100   0.022271339    0.022271339    0.017947505    0.0014630387 
+     22000         100   0.019277834    0.019277834    0.015483116    0.00058751407
+     22100         100   0.019997809    0.019997809    0.015919504    0.00064176101
+     22200         100   0.015870543    0.015870543    0.01244838     0.0004205505 
+     22300         100   0.011797587    0.011797587    0.0096491363   0.00034907063
+     22400         100   0.010745212    0.010745212    0.008874218    0.00035427537
+     22500         100   0.0082372399   0.0082372399   0.0071217811   0.00028179943
+     22600         100   0.007942576    0.007942576    0.0067248822   0.001507115  
+     22700         100   0.0061733667   0.0061733667   0.0053092324   0.00056018554
+     22800         100   0.0058287651   0.0058287651   0.004972189    0.00023807695
+     22900         100   0.0051352339   0.0051352339   0.004324157    0.00020849263
+     23000         100   0.0040107769   0.0040107769   0.0035769703   0.00022626101
+     23100         100   0.0040288854   0.0040288854   0.0034355474   0.00019107621
+     23200         100   0.003277858    0.003277858    0.0030013165   0.00016119888
+     23300         100   0.0033633749   0.0033633749   0.0030188927   0.00014459404
+     23400         100   0.003468042    0.003468042    0.0030079205   0.00013778427
+     23500         100   0.0027616702   0.0027616702   0.0024994596   0.00011834915
+     23600         100   0.0022531303   0.0022531303   0.0021182802   0.0002279623 
+     23700         100   0.002067768    0.002067768    0.0019631752   0.00014341503
+     23800         100   0.0020069255   0.0020069255   0.0019209587   0.00010673435
+     23900         100   0.0019630617   0.0019630617   0.0018748221   0.00011856923
+     24000         100   0.0018800646   0.0018800646   0.0018190347   0.00010707562
+     24100         100   0.0018028137   0.0018028137   0.0017067233   0.00010884117
+     24200         100   0.0017278932   0.0017278932   0.0016251004   0.00013664683
+     24300         100   0.0016373288   0.0016373288   0.0015529481   0.00010025414
+     24400         100   0.0019876848   0.0019876848   0.0016912033   0.00011235942
+     24500         100   0.0013677345   0.0013677345   0.0012839488   7.8669645e-05
+     24600         100   0.0012852614   0.0012852614   0.0012065052   0.00010172361
+     24700         100   0.0011145002   0.0011145002   0.0010748344   7.5021689e-05
+     24800         100   0.0012860792   0.0012860792   0.0011429675   5.7939624e-05
+     24900         100   0.00097198499  0.00097198499  0.00096175911  5.443837e-05 
+     25000         100   0.00096224466  0.00096224466  0.00095159089  5.4245409e-05
+Loop time of 0.0846408 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 25519602.289 tau/day, 59073.153 timesteps/s, 5.907 Matom-step/s
+82.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0035473  | 0.0055294  | 0.0082454  |   2.7 |  6.53
+Neigh   | 0.0016391  | 0.0022521  | 0.0028115  |   1.1 |  2.66
+Comm    | 0.014697   | 0.021565   | 0.029045   |   4.1 | 25.48
+Output  | 0.0010785  | 0.00132    | 0.0014171  |   0.4 |  1.56
+Modify  | 0.0059648  | 0.01618    | 0.027615   |   7.9 | 19.12
+Other   |            | 0.03779    |            |       | 44.65
+
+Nlocal:             25 ave          56 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:            5.5 ave          12 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:             40 ave         101 max           0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 160
+Ave neighs/atom = 1.6
+Neighbor list builds = 275
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/granregion/log.15Sep22.granregion.funnel.g++.1

@@ -0,0 +1,633 @@
+LAMMPS (15 Sep 2022)
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable	name string funnel_pour
+
+thermo_modify	flush yes
+units 		si
+variable	PI equal 3.141592653589
+variable	seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	xlo equal 10
+variable	xhi equal 40
+variable	ylo equal 10
+variable	yhi equal 40
+variable	zlo equal -20
+variable	zhi equal 50
+
+variable	xc equal 25
+variable	yc equal 25
+
+variable	zconehi equal 50
+variable	zconelo equal 10
+variable	zcyllo equal 0
+variable	radconelo equal 2
+variable	radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable 	skin equal ${rhi}
+variable 	skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	density equal 1.0
+variable	EYoung equal 10^5
+variable 	Poisson equal 2.0/7.0
+variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+0.285714285714286))
+
+variable	gravity equal 1.0
+
+variable	reff equal 0.5*(${rhi}+${rlo})
+variable	reff equal 0.5*(0.5+${rlo})
+variable	reff equal 0.5*(0.5+0.25)
+variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable        kt equal 4.0*${GShear}/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable	a equal (-2.0*log(${coeffRes})/${PI})^2
+variable	a equal (-2.0*log(0.1)/${PI})^2
+variable	a equal (-2.0*log(0.1)/3.141592653589)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 903.503751814138*0.5
+
+variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable	dt equal ${tcol}*0.05
+variable	dt equal 0.00210943016014969*0.05
+timestep	${dt}
+timestep	0.000105471508007485
+
+###############################################
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		off
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 -20 ${zhi}
+region		boxreg block 10 40 10 40 -20 50
+create_box	1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.5 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0
+  ghost atom cutoff = 0
+  binsize = 30, bins = 1 1 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/multi/newtoff
+      stencil: full/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
+
+region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
+region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
+
+region		hopreg union 2 conereg cylreg
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+
+fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+
+#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:896)
+thermo_modify	flush yes lost warn
+
+# Initial run to fill up the cone
+
+run		20000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
+   Step          CPU          Atoms        KinEng    
+         0   0                      0  -0            
+      1000   0.39961733          2000  -0            
+      2000   0.61811961          2000  -0            
+      3000   0.83512725          2000  -0            
+      4000   1.0492881           2000  -0            
+      5000   1.2650657           2000  -0            
+      6000   1.479921            2000  -0            
+      7000   1.6970993           2000  -0            
+      8000   1.9107924           2000  -0            
+      9000   2.1251713           2000  -0            
+     10000   2.3403682           2000  -0            
+     11000   2.549912            2000  -0            
+     12000   2.7584788           2000  -0            
+     13000   2.9712482           2000  -0            
+     14000   3.1877015           2000  -0            
+     15000   3.4017175           2000  -0            
+     16000   3.6127477           2000  -0            
+     17000   3.8250134           2000  -0            
+     18000   4.0320643           2000  -0            
+     19000   4.2371057           2000  -0            
+     20000   4.4450882           2000  -0            
+Loop time of 4.44512 on 1 procs for 20000 steps with 2000 atoms
+
+98.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.40438    | 0.40438    | 0.40438    |   0.0 |  9.10
+Neigh   | 0.078634   | 0.078634   | 0.078634   |   0.0 |  1.77
+Comm    | 0.01999    | 0.01999    | 0.01999    |   0.0 |  0.45
+Output  | 0.00069031 | 0.00069031 | 0.00069031 |   0.0 |  0.02
+Modify  | 3.795      | 3.795      | 3.795      |   0.0 | 85.38
+Other   |            | 0.1464     |            |       |  3.29
+
+Nlocal:           2000 ave        2000 max        2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1607 ave        1607 max        1607 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1607
+Ave neighs/atom = 0.8035
+Neighbor list builds = 71
+Dangerous builds = 0
+unfix 		ins
+run		150000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
+   Step          CPU          Atoms        KinEng    
+     20000   0                   2000   6652.2957    
+     21000   0.2135317           2000   6807.2201    
+     22000   0.4235523           2000   6973.9359    
+     23000   0.63502794          2000   7142.3648    
+     24000   0.84593615          2000   7276.9717    
+     25000   1.0580291           2000   7369.4191    
+     26000   1.2719892           2000   7497.6526    
+     27000   1.4843056           2000   7638.946     
+     28000   1.9685336           2000   7780.0339    
+     29000   2.1850097           2000   7881.8177    
+     30000   2.4033006           2000   7967.2641    
+     31000   2.6219694           2000   7994.9273    
+     32000   2.8455468           2000   7937.0671    
+     33000   3.0720066           2000   7774.0508    
+     34000   3.3070513           2000   7591.1491    
+     35000   3.5468777           2000   7357.5176    
+     36000   3.7908265           2000   7147.2024    
+     37000   4.0388657           2000   6979.1604    
+     38000   4.2873223           2000   6813.2152    
+     39000   4.5424244           2000   6660.2701    
+     40000   4.8055367           2000   6502.8957    
+     41000   5.0754561           2000   6324.3951    
+     42000   5.3564118           2000   6132.7516    
+     43000   5.6357256           2000   5913.1841    
+     44000   5.9130645           2000   5732.2095    
+     45000   6.1943539           2000   5508.8322    
+     46000   6.4862302           2000   5306.8932    
+     47000   6.7796417           2000   5152.0521    
+     48000   7.0750069           2000   5028.2274    
+     49000   7.3705252           2000   4896.102     
+     50000   7.6693894           2000   4723.5189    
+     51000   7.9685182           2000   4583.7526    
+     52000   8.2774033           2000   4447.0187    
+     53000   8.591482            2000   4303.2307    
+     54000   8.9156439           2000   4168.5251    
+     55000   9.2437364           2000   4036.9704    
+     56000   9.5745684           2000   3901.1183    
+     57000   9.9173689           2000   3716.7071    
+     58000   10.270229           2000   3473.5422    
+     59000   10.629101           2000   3245.1223    
+     60000   10.989479           2000   3039.7845    
+     61000   11.349843           2000   2780.0187    
+     62000   11.716916           2000   2577.3345    
+     63000   12.093666           2000   2346.2488    
+     64000   12.474788           2000   2116.7298    
+     65000   12.861438           2000   1903.7828    
+     66000   13.25464            2000   1631.1676    
+     67000   13.658382           2000   1431.0198    
+     68000   14.067584           2000   1212.875     
+     69000   14.480877           2000   995.45046    
+     70000   14.894765           2000   811.54766    
+     71000   15.309158           2000   624.08622    
+     72000   15.732937           2000   471.00862    
+     73000   16.158388           2000   358.33486    
+     74000   16.583847           2000   284.39416    
+     75000   17.008335           2000   234.26671    
+     76000   17.429582           2000   185.61836    
+     77000   17.852799           2000   152.95918    
+     78000   18.276783           2000   122.49023    
+     79000   18.697016           2000   102.29396    
+     80000   19.12318            2000   86.284684    
+     81000   19.54992            2000   73.984781    
+     82000   19.986149           2000   63.042918    
+     83000   20.430305           2000   53.338428    
+     84000   20.876061           2000   45.89585     
+     85000   21.32714            2000   40.412826    
+     86000   21.781352           2000   34.183381    
+     87000   22.238656           2000   29.671524    
+     88000   22.698093           2000   26.90414     
+     89000   23.160614           2000   24.362631    
+     90000   23.630639           2000   21.887341    
+     91000   24.095463           2000   19.985662    
+     92000   24.570659           2000   18.728162    
+     93000   25.047431           2000   16.99941     
+     94000   25.549041           2000   15.71941     
+     95000   26.03281            2000   14.744057    
+     96000   26.513659           2000   14.214918    
+     97000   26.998918           2000   13.450182    
+     98000   27.486584           2000   12.79222     
+     99000   27.986785           2000   12.10595     
+    100000   28.48799            2000   11.281863    
+    101000   28.986622           2000   10.025419    
+    102000   29.491312           2000   9.9574468    
+    103000   29.999421           2000   9.4078117    
+    104000   30.507211           2000   8.9079161    
+    105000   31.016484           2000   8.6269302    
+    106000   31.527511           2000   8.5512649    
+    107000   32.042612           2000   8.4703948    
+    108000   32.555041           2000   8.2747542    
+    109000   33.07064            2000   8.2895118    
+    110000   33.593773           2000   8.1785613    
+    111000   34.107129           2000   7.8443234    
+    112000   34.619185           2000   7.7436124    
+    113000   35.13418            2000   7.8118604    
+    114000   35.653352           2000   7.3806177    
+    115000   36.179577           2000   7.0857235    
+    116000   36.69882            2000   7.1346752    
+    117000   37.224612           2000   7.0653751    
+    118000   37.756738           2000   6.6314104    
+    119000   38.283151           2000   6.2169614    
+    120000   38.808288           2000   5.8988829    
+    121000   39.334913           2000   5.4197277    
+    122000   39.862081           2000   4.6381303    
+    123000   40.390252           2000   4.4949206    
+    124000   40.920744           2000   4.4261118    
+    125000   41.4469             2000   4.4223703    
+    126000   41.977937           2000   4.4858898    
+    127000   42.51483            2000   4.3312536    
+    128000   43.046324           2000   3.7124973    
+    129000   43.573687           2000   3.5467396    
+    130000   44.103102           2000   3.5104139    
+    131000   44.629869           2000   3.5725612    
+    132000   45.156621           2000   3.669455     
+    133000   45.69364            2000   3.6168912    
+    134000   46.23133            2000   3.3598517    
+    135000   46.765487           2000   3.3743407    
+    136000   47.323693           2000   3.1109764    
+    137000   47.881617           2000   3.0720146    
+    138000   48.439179           2000   3.1303776    
+    139000   49.001417           2000   3.2052806    
+    140000   49.558061           2000   2.8958882    
+    141000   50.097789           2000   2.9931572    
+    142000   50.636089           2000   3.0967832    
+    143000   51.175873           2000   3.0576365    
+    144000   51.706799           2000   3.2016943    
+    145000   52.239356           2000   3.3817709    
+    146000   52.769944           2000   3.4527239    
+    147000   53.30872            2000   3.5928733    
+    148000   53.847762           2000   3.7784682    
+    149000   54.387455           2000   3.6587944    
+    150000   54.931594           2000   3.7945669    
+    151000   55.470076           2000   3.5551557    
+    152000   56.01448            2000   3.6248848    
+    153000   56.552259           2000   3.7361463    
+    154000   57.092655           2000   3.8534319    
+    155000   57.635767           2000   4.0101408    
+    156000   58.180249           2000   3.7670652    
+    157000   58.724032           2000   3.1487676    
+    158000   59.262015           2000   2.980076     
+    159000   59.794312           2000   3.0350592    
+    160000   60.331617           2000   3.125389     
+    161000   60.861827           2000   2.7516115    
+    162000   61.396691           2000   2.413911     
+    163000   61.930145           2000   2.297713     
+    164000   62.466983           2000   2.3190806    
+    165000   63.00535            2000   2.2868879    
+    166000   63.546881           2000   2.1658547    
+    167000   64.091461           2000   1.7511071    
+    168000   64.63141            2000   1.4112478    
+    169000   65.17459            2000   1.3623558    
+    170000   65.719571           2000   1.3701579    
+Loop time of 65.7196 on 1 procs for 150000 steps with 2000 atoms
+
+98.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 32.424     | 32.424     | 32.424     |   0.0 | 49.34
+Neigh   | 0.65326    | 0.65326    | 0.65326    |   0.0 |  0.99
+Comm    | 0.14207    | 0.14207    | 0.14207    |   0.0 |  0.22
+Output  | 0.26326    | 0.26326    | 0.26326    |   0.0 |  0.40
+Modify  | 31.109     | 31.109     | 31.109     |   0.0 | 47.34
+Other   |            | 1.128      |            |       |  1.72
+
+Nlocal:           2000 ave        2000 max        2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          15308 ave       15308 max       15308 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15308
+Ave neighs/atom = 7.654
+Neighbor list builds = 367
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region	  	cylreg delete
+region		hopreg delete
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
+
+region		hopreg union 2 cylreg conereg
+
+unfix		hopper3
+fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run		100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
+   Step          CPU          Atoms        KinEng    
+    170000   0                   2000   1.3701579    
+    171000   0.54961146          2000   2.3724823    
+    172000   1.0905775           2000   3.5881441    
+    173000   1.6190656           2000   5.3771633    
+    174000   2.1428619           2000   7.5896471    
+    175000   2.6623327           2000   10.77251     
+    176000   3.1738773           2000   14.806868    
+    177000   3.6751053           2000   19.607624    
+    178000   4.17465             2000   25.426227    
+    179000   4.6736143           2000   32.23584     
+    180000   5.1769137           2000   39.930468    
+    181000   5.6766809           2000   47.686304    
+    182000   6.1722504           2000   56.506806    
+    183000   6.6603586           2000   66.514326    
+    184000   7.1473381           2000   77.554644    
+    185000   7.6343824           2000   89.224002    
+    186000   8.1170225           2000   102.07846    
+    187000   8.598305            2000   116.08141    
+    188000   9.0708108           2000   130.97964    
+    189000   9.5435695           2000   146.77806    
+    190000   10.015069           2000   162.79858    
+    191000   10.480992           2000   179.02052    
+    192000   10.941896           2000   196.26683    
+    193000   11.398748           2000   214.38928    
+    194000   11.856098           2000   232.32068    
+    195000   12.314324           2000   251.74644    
+    196000   12.765746           2000   272.25231    
+    197000   13.216453           2000   294.64075    
+    198000   13.663698           2000   318.32895    
+    199000   14.109901           2000   342.44005    
+    200000   14.560399           2000   368.35469    
+    201000   15.008158           2000   395.2465     
+    202000   15.460487           2000   422.63599    
+    203000   15.913115           2000   450.45248    
+    204000   16.363656           2000   479.60812    
+    205000   16.816929           2000   510.44155    
+    206000   17.265488           2000   543.25751    
+    207000   17.707782           2000   577.35928    
+    208000   18.151051           2000   612.29718    
+    209000   18.588363           2000   647.8951     
+    210000   19.027167           2000   683.79409    
+    211000   19.463213           2000   720.36556    
+    212000   19.901783           2000   759.27331    
+    213000   20.340436           2000   798.27302    
+    214000   20.775782           2000   837.93849    
+    215000   21.207465           2000   877.92945    
+    216000   21.641572           2000   919.62532    
+    217000   22.077351           2000   962.83509    
+    218000   22.517089           2000   1008.5243    
+    219000   22.948683           2000   1054.5769    
+    220000   23.381029           2000   1103.1843    
+    221000   23.809214           2000   1153.0349    
+    222000   24.246127           2000   1204.5599    
+    223000   24.677676           2000   1257.1367    
+    224000   25.113989           2000   1308.6735    
+WARNING: Lost atoms: original 2000 current 1999 (../thermo.cpp:486)
+    225000   25.549621           1999   1360.1205    
+    226000   25.977155           1998   1404.8405    
+    227000   26.406475           1996   1448.4869    
+    228000   26.832152           1992   1491.8112    
+    229000   27.25327            1985   1518.7013    
+    230000   27.672907           1971   1507.6699    
+    231000   28.086761           1965   1533.5096    
+    232000   28.500134           1948   1489.4128    
+    233000   28.912212           1933   1477.4536    
+    234000   29.320197           1915   1425.8398    
+    235000   29.723669           1904   1410.1451    
+    236000   30.124339           1892   1401.7595    
+    237000   30.523539           1880   1368.893     
+    238000   30.919483           1868   1341.8885    
+    239000   31.313194           1850   1286.7968    
+    240000   31.711659           1833   1219.5123    
+    241000   32.106468           1820   1173.3608    
+    242000   32.505486           1806   1106.0727    
+    243000   32.905579           1788   1035.912     
+    244000   33.303155           1779   1021.6147    
+    245000   33.696614           1767   969.40032    
+    246000   34.083545           1757   939.12022    
+    247000   34.472486           1739   840.9396     
+    248000   34.858907           1730   822.06575    
+    249000   35.248061           1719   762.11057    
+    250000   35.639608           1707   708.50308    
+    251000   36.029812           1700   692.12647    
+    252000   36.428881           1697   694.5812     
+    253000   36.821304           1686   652.36951    
+    254000   37.203008           1682   662.95256    
+    255000   37.576678           1677   637.34619    
+    256000   37.952398           1672   630.71277    
+    257000   38.336834           1669   641.87365    
+    258000   38.719421           1665   635.862      
+    259000   39.104236           1664   658.5339     
+    260000   39.484223           1662   669.95468    
+    261000   39.861203           1660   676.93495    
+    262000   40.240183           1657   681.72646    
+    263000   40.614974           1655   687.4078     
+    264000   40.99447            1651   681.61352    
+    265000   41.368018           1647   673.20622    
+    266000   41.740288           1644   677.30073    
+    267000   42.111704           1641   671.05897    
+    268000   42.479868           1639   689.55776    
+    269000   42.851008           1637   711.98809    
+    270000   43.22438            1633   705.29974    
+Loop time of 43.2244 on 1 procs for 100000 steps with 1633 atoms
+
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.312     | 22.312     | 22.312     |   0.0 | 51.62
+Neigh   | 0.47451    | 0.47451    | 0.47451    |   0.0 |  1.10
+Comm    | 0.093822   | 0.093822   | 0.093822   |   0.0 |  0.22
+Output  | 0.0028326  | 0.0028326  | 0.0028326  |   0.0 |  0.01
+Modify  | 19.626     | 19.626     | 19.626     |   0.0 | 45.40
+Other   |            | 0.7152     |            |       |  1.65
+
+Nlocal:           1633 ave        1633 max        1633 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          11358 ave       11358 max       11358 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 11358
+Ave neighs/atom = 6.955297
+Neighbor list builds = 244
+Dangerous builds = 0
+Total wall time: 0:01:53

examples/granregion/log.15Sep22.granregion.funnel.g++.4

@@ -0,0 +1,633 @@
+LAMMPS (15 Sep 2022)
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable	name string funnel_pour
+
+thermo_modify	flush yes
+units 		si
+variable	PI equal 3.141592653589
+variable	seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	xlo equal 10
+variable	xhi equal 40
+variable	ylo equal 10
+variable	yhi equal 40
+variable	zlo equal -20
+variable	zhi equal 50
+
+variable	xc equal 25
+variable	yc equal 25
+
+variable	zconehi equal 50
+variable	zconelo equal 10
+variable	zcyllo equal 0
+variable	radconelo equal 2
+variable	radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable 	skin equal ${rhi}
+variable 	skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	density equal 1.0
+variable	EYoung equal 10^5
+variable 	Poisson equal 2.0/7.0
+variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+0.285714285714286))
+
+variable	gravity equal 1.0
+
+variable	reff equal 0.5*(${rhi}+${rlo})
+variable	reff equal 0.5*(0.5+${rlo})
+variable	reff equal 0.5*(0.5+0.25)
+variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable        kt equal 4.0*${GShear}/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable	a equal (-2.0*log(${coeffRes})/${PI})^2
+variable	a equal (-2.0*log(0.1)/${PI})^2
+variable	a equal (-2.0*log(0.1)/3.141592653589)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 903.503751814138*0.5
+
+variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable	dt equal ${tcol}*0.05
+variable	dt equal 0.00210943016014969*0.05
+timestep	${dt}
+timestep	0.000105471508007485
+
+###############################################
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		off
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 -20 ${zhi}
+region		boxreg block 10 40 10 40 -20 50
+create_box	1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+  1 by 1 by 4 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.5 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0
+  ghost atom cutoff = 0
+  binsize = 30, bins = 1 1 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/multi/newtoff
+      stencil: full/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
+
+region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
+region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
+
+region		hopreg union 2 conereg cylreg
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+
+fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+
+#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:896)
+thermo_modify	flush yes lost warn
+
+# Initial run to fill up the cone
+
+run		20000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
+   Step          CPU          Atoms        KinEng    
+         0   0                      0  -0            
+      1000   0.4194951           2000  -0            
+      2000   0.61516729          2000  -0            
+      3000   0.80702516          2000  -0            
+      4000   0.99253349          2000  -0            
+      5000   1.172741            2000  -0            
+      6000   1.3484682           2000  -0            
+      7000   1.5206253           2000  -0            
+      8000   1.6875025           2000  -0            
+      9000   1.8503087           2000  -0            
+     10000   2.0125622           2000  -0            
+     11000   2.0890872           2000  -0            
+     12000   2.1663582           2000  -0            
+     13000   2.2430386           2000  -0            
+     14000   2.320045            2000  -0            
+     15000   2.3989769           2000  -0            
+     16000   2.4824747           2000  -0            
+     17000   2.5693391           2000  -0            
+     18000   2.6595183           2000  -0            
+     19000   2.752627            2000  -0            
+     20000   2.8503071           2000  -0            
+Loop time of 2.85034 on 4 procs for 20000 steps with 2000 atoms
+
+98.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.04057    | 0.088166   | 0.18377    |  18.9 |  3.09
+Neigh   | 0.0072649  | 0.014273   | 0.025073   |   5.5 |  0.50
+Comm    | 0.097843   | 0.19506    | 0.29871    |  19.9 |  6.84
+Output  | 0.00099986 | 0.0018246  | 0.0023299  |   1.2 |  0.06
+Modify  | 0.68567    | 1.1174     | 1.9527     |  46.8 | 39.20
+Other   |            | 1.434      |            |       | 50.30
+
+Nlocal:            500 ave         510 max         493 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:            154 ave         227 max          79 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:          415.5 ave         610 max         258 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 1662
+Ave neighs/atom = 0.831
+Neighbor list builds = 71
+Dangerous builds = 0
+unfix 		ins
+run		150000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
+   Step          CPU          Atoms        KinEng    
+     20000   0                   2000   6652.2957    
+     21000   0.069761009         2000   6807.2201    
+     22000   0.14277925          2000   6973.9359    
+     23000   0.21755553          2000   7142.3648    
+     24000   0.29656838          2000   7276.9717    
+     25000   0.3791331           2000   7369.4191    
+     26000   0.46663378          2000   7497.6526    
+     27000   0.55670237          2000   7638.946     
+     28000   0.65212555          2000   7780.0339    
+     29000   0.75032507          2000   7881.8177    
+     30000   0.85580942          2000   7967.2641    
+     31000   0.93204785          2000   7994.9273    
+     32000   1.0168325           2000   7937.0672    
+     33000   1.1081585           2000   7774.0508    
+     34000   1.2084122           2000   7591.1511    
+     35000   1.3164174           2000   7357.5032    
+     36000   1.4326847           2000   7147.3776    
+     37000   1.5548919           2000   6980.0719    
+     38000   1.6806183           2000   6813.0872    
+     39000   1.8171138           2000   6657.0693    
+     40000   1.9655069           2000   6505.1155    
+     41000   2.0788398           2000   6330.2864    
+     42000   2.1972941           2000   6147.8022    
+     43000   2.3180177           2000   5932.9244    
+     44000   2.4424194           2000   5755.296     
+     45000   2.5679759           2000   5511.622     
+     46000   2.7042099           2000   5332.3171    
+     47000   2.8436403           2000   5162.4926    
+     48000   2.983017            2000   5044.5764    
+     49000   3.1228322           2000   4901.1141    
+     50000   3.2614172           2000   4731.1949    
+     51000   3.3835559           2000   4575.418     
+     52000   3.5097034           2000   4428.9425    
+     53000   3.6438561           2000   4291.7282    
+     54000   3.7823058           2000   4154.1885    
+     55000   3.9269393           2000   3994.9402    
+     56000   4.0761939           2000   3855.5977    
+     57000   4.2262191           2000   3672.9504    
+     58000   4.3809045           2000   3435.3395    
+     59000   4.5439971           2000   3200.7379    
+     60000   4.7111867           2000   2986.5411    
+     61000   4.8700167           2000   2747.3628    
+     62000   5.030656            2000   2542.0805    
+     63000   5.1932098           2000   2336.7687    
+     64000   5.3585095           2000   2151.6388    
+     65000   5.5278279           2000   1933.6773    
+     66000   5.7032072           2000   1699.0747    
+     67000   5.8804545           2000   1467.7209    
+     68000   6.0598984           2000   1227.3577    
+     69000   6.2471961           2000   1016.2766    
+     70000   6.4413532           2000   812.90843    
+     71000   6.615215            2000   632.88108    
+     72000   6.7897335           2000   470.67731    
+     73000   6.964705            2000   360.47748    
+     74000   7.1361808           2000   286.10584    
+     75000   7.3068097           2000   229.70386    
+     76000   7.4771974           2000   179.62654    
+     77000   7.6485358           2000   142.40417    
+     78000   7.8200771           2000   113.55745    
+     79000   7.9923688           2000   93.787669    
+     80000   8.164219            2000   80.646319    
+     81000   8.3372059           2000   70.944319    
+     82000   8.5130035           2000   59.2275      
+     83000   8.6877383           2000   49.633808    
+     84000   8.8675712           2000   42.882698    
+     85000   9.0509682           2000   36.841824    
+     86000   9.2393665           2000   31.776681    
+     87000   9.4296116           2000   28.25076     
+     88000   9.622196            2000   25.228966    
+     89000   9.8176023           2000   22.593627    
+     90000   10.01325            2000   21.15796     
+     91000   10.204474           2000   19.941629    
+     92000   10.399553           2000   18.375654    
+     93000   10.596683           2000   17.056701    
+     94000   10.796988           2000   16.192511    
+     95000   10.998545           2000   15.572922    
+     96000   11.200614           2000   14.827788    
+     97000   11.402484           2000   13.919613    
+     98000   11.606219           2000   13.19525     
+     99000   11.81042            2000   11.993376    
+    100000   12.018294           2000   11.258787    
+    101000   12.223702           2000   10.641688    
+    102000   12.432026           2000   10.430435    
+    103000   12.640962           2000   9.518069     
+    104000   12.849109           2000   9.1332086    
+    105000   13.05872            2000   9.2151611    
+    106000   13.269956           2000   9.0035132    
+    107000   13.481882           2000   8.7835861    
+    108000   13.693895           2000   8.5124479    
+    109000   13.906381           2000   8.2975453    
+    110000   14.120217           2000   8.3483043    
+    111000   14.332078           2000   8.4658572    
+    112000   14.54349            2000   8.4771784    
+    113000   14.755719           2000   7.8937975    
+    114000   14.968619           2000   7.2472953    
+    115000   15.180485           2000   6.5812074    
+    116000   15.394405           2000   5.5651566    
+    117000   15.607523           2000   5.3015807    
+    118000   15.821873           2000   5.0133941    
+    119000   16.035675           2000   4.8746036    
+    120000   16.24964            2000   4.9133073    
+    121000   16.462102           2000   4.3337392    
+    122000   16.676371           2000   4.3374836    
+    123000   16.890252           2000   4.3721818    
+    124000   17.106594           2000   4.3894508    
+    125000   17.321433           2000   4.1811774    
+    126000   17.536692           2000   4.3011002    
+    127000   17.748238           2000   4.442228     
+    128000   17.962609           2000   4.6170394    
+    129000   18.175315           2000   4.8184318    
+    130000   18.389056           2000   4.8442096    
+    131000   18.600872           2000   4.9668117    
+    132000   18.81412            2000   4.8364562    
+    133000   19.027514           2000   4.6658645    
+    134000   19.23975            2000   4.5758487    
+    135000   19.451085           2000   4.7251949    
+    136000   19.663874           2000   4.5846492    
+    137000   19.87624            2000   4.7565986    
+    138000   20.088654           2000   4.8186623    
+    139000   20.29935            2000   4.6571647    
+    140000   20.510911           2000   4.0730143    
+    141000   20.722072           2000   4.0605542    
+    142000   20.933113           2000   4.1457179    
+    143000   21.143916           2000   4.3418042    
+    144000   21.353873           2000   4.0323813    
+    145000   21.567015           2000   3.8064958    
+    146000   21.781334           2000   3.1802044    
+    147000   21.996799           2000   2.7947641    
+    148000   22.209808           2000   2.7384164    
+    149000   22.423177           2000   2.7428829    
+    150000   22.638044           2000   2.7802186    
+    151000   22.851676           2000   2.6703451    
+    152000   23.065354           2000   2.3357647    
+    153000   23.278882           2000   1.9855305    
+    154000   23.494254           2000   1.9442713    
+    155000   23.708192           2000   1.7348027    
+    156000   23.923005           2000   1.5699942    
+    157000   24.13827            2000   1.5224944    
+    158000   24.352068           2000   1.4850914    
+    159000   24.565616           2000   1.4461048    
+    160000   24.779118           2000   1.3759525    
+    161000   24.99111            2000   0.83754463   
+    162000   25.205935           2000   0.7952922    
+    163000   25.420817           2000   0.69670143   
+    164000   25.632672           2000   0.66253723   
+    165000   25.846901           2000   0.64602969   
+    166000   26.060074           2000   0.60229858   
+    167000   26.273714           2000   0.5757589    
+    168000   26.484855           2000   0.5996023    
+    169000   26.698151           2000   0.62130448   
+    170000   26.911208           2000   0.63888277   
+Loop time of 26.9112 on 4 procs for 150000 steps with 2000 atoms
+
+95.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.5517     | 8.6135     | 10.872     |  82.7 | 32.01
+Neigh   | 0.092491   | 0.15402    | 0.19598    |   9.7 |  0.57
+Comm    | 2.0054     | 3.8686     | 4.6494     |  55.0 | 14.38
+Output  | 0.0047033  | 0.0096766  | 0.016452   |   4.6 |  0.04
+Modify  | 5.6498     | 7.9588     | 9.4012     |  49.7 | 29.57
+Other   |            | 6.307      |            |       | 23.43
+
+Nlocal:            500 ave         538 max         419 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Nghost:          445.5 ave         688 max         200 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:        4500.25 ave        5610 max        3443 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 18001
+Ave neighs/atom = 9.0005
+Neighbor list builds = 362
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region	  	cylreg delete
+region		hopreg delete
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
+
+region		hopreg union 2 cylreg conereg
+
+unfix		hopper3
+fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run		100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
+   Step          CPU          Atoms        KinEng    
+    170000   0                   2000   0.63888277   
+    171000   0.21419748          2000   1.4139245    
+    172000   0.42844271          2000   2.2400138    
+    173000   0.64333145          2000   3.8034979    
+    174000   0.85456696          2000   6.116727     
+    175000   1.0672981           2000   8.9536458    
+    176000   1.2790911           2000   12.74348     
+    177000   1.491721            2000   17.410816    
+    178000   1.7033452           2000   22.879174    
+    179000   1.9168047           2000   28.966022    
+    180000   2.1329071           2000   35.449239    
+    181000   2.3490841           2000   42.694882    
+    182000   2.565508            2000   50.913279    
+    183000   2.780369            2000   60.098465    
+    184000   2.9967771           2000   70.133474    
+    185000   3.2116891           2000   80.950013    
+    186000   3.4248923           2000   92.495525    
+    187000   3.6394206           2000   104.83034    
+    188000   3.8527533           2000   118.04659    
+    189000   4.0650838           2000   132.7403     
+    190000   4.2781031           2000   148.31955    
+    191000   4.476226            2000   164.26321    
+    192000   4.6750263           2000   180.6933     
+    193000   4.8710737           2000   197.72012    
+    194000   5.0677642           2000   215.43637    
+    195000   5.2639974           2000   234.29738    
+    196000   5.4599746           2000   254.03407    
+    197000   5.6534894           2000   274.58626    
+    198000   5.8462402           2000   296.88915    
+    199000   6.0400194           2000   320.45001    
+    200000   6.2329415           2000   344.75891    
+    201000   6.4235068           2000   370.14016    
+    202000   6.6142055           2000   395.72827    
+    203000   6.8048206           2000   420.42026    
+    204000   6.9987454           2000   446.08079    
+    205000   7.1925778           2000   473.62963    
+    206000   7.3846227           2000   501.05693    
+    207000   7.5775122           2000   530.40427    
+    208000   7.77052             2000   560.62015    
+    209000   7.964984            2000   593.00113    
+    210000   8.1601405           2000   626.36661    
+    211000   8.3504978           2000   661.34861    
+    212000   8.5425141           2000   697.41001    
+    213000   8.736112            2000   735.12299    
+    214000   8.9267615           2000   773.89126    
+    215000   9.1154738           2000   813.83268    
+    216000   9.3019826           2000   854.63669    
+    217000   9.4878433           2000   896.59089    
+    218000   9.6739682           2000   938.70251    
+    219000   9.8566518           2000   982.10773    
+    220000   10.042289           2000   1025.2953    
+    221000   10.227275           2000   1069.8382    
+    222000   10.412363           2000   1115.4449    
+    223000   10.602757           2000   1161.6742    
+    224000   10.789101           2000   1211.289     
+    225000   10.974854           2000   1262.8074    
+    226000   11.157089           2000   1316.6353    
+    227000   11.337044           2000   1370.7434    
+WARNING: Lost atoms: original 2000 current 1991 (../thermo.cpp:486)
+    228000   11.518718           1991   1382.0924    
+    229000   11.700488           1986   1407.1543    
+    230000   11.883057           1975   1415.708     
+    231000   12.063962           1968   1430.6498    
+    232000   12.246917           1957   1421.0352    
+    233000   12.429345           1939   1376.0322    
+    234000   12.6113             1925   1350.1292    
+    235000   12.791233           1912   1337.0529    
+    236000   12.968444           1893   1273.2219    
+    237000   13.146668           1879   1207.0473    
+    238000   13.327542           1861   1132.0109    
+    239000   13.50936            1846   1083.1042    
+    240000   13.693504           1826   1004.3265    
+    241000   13.863443           1819   989.36186    
+    242000   14.03294            1812   983.26132    
+    243000   14.20032            1805   985.79932    
+    244000   14.366236           1794   936.34844    
+    245000   14.532759           1784   889.17423    
+    246000   14.703029           1770   846.65018    
+    247000   14.873941           1753   751.16306    
+    248000   15.045272           1740   709.23095    
+    249000   15.217896           1732   687.61586    
+    250000   15.388727           1721   638.82967    
+    251000   15.558032           1714   618.71543    
+    252000   15.725309           1709   611.25444    
+    253000   15.888727           1705   606.6846     
+    254000   16.050605           1702   601.7236     
+    255000   16.212982           1697   575.97244    
+    256000   16.378352           1695   577.1712     
+    257000   16.547488           1691   576.93668    
+    258000   16.718964           1688   586.63687    
+    259000   16.892601           1686   581.52487    
+    260000   17.066036           1682   566.49544    
+    261000   17.22488            1681   586.18628    
+    262000   17.379249           1678   582.11927    
+    263000   17.534079           1675   589.96041    
+    264000   17.690288           1672   577.55581    
+    265000   17.847805           1669   570.45998    
+    266000   18.006261           1666   574.0576     
+    267000   18.1674             1662   578.07385    
+    268000   18.326753           1660   587.65705    
+    269000   18.488052           1657   584.43358    
+    270000   18.647474           1654   591.22601    
+Loop time of 18.6475 on 4 procs for 100000 steps with 1654 atoms
+
+94.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.7714     | 6.1879     | 8.8765     |  88.8 | 33.18
+Neigh   | 0.094692   | 0.11244    | 0.13298    |   4.6 |  0.60
+Comm    | 1.2471     | 2.918      | 3.5873     |  57.0 | 15.65
+Output  | 0.0013438  | 0.0067176  | 0.014709   |   6.0 |  0.04
+Modify  | 4.4355     | 5.0416     | 5.5692     |  21.9 | 27.04
+Other   |            | 4.381      |            |       | 23.49
+
+Nlocal:          413.5 ave         429 max         408 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:         408.25 ave         653 max         182 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:        3486.25 ave        4367 max        2213 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 13945
+Ave neighs/atom = 8.4310762
+Neighbor list builds = 227
+Dangerous builds = 0
+Total wall time: 0:00:48

examples/granregion/log.15Sep22.granregion.mixer.g++.1

@@ -0,0 +1,632 @@
+LAMMPS (15 Sep 2022)
+variable	name string mixer
+
+thermo_modify	flush yes
+variable	seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable	rlo equal 0.3
+variable	rhi equal 0.6
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.3
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.6
+variable 	skin equal ${rhi}
+variable 	skin equal 0.6
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	kn equal 10^5
+variable	kt equal 0.2*${kn}
+variable	kt equal 0.2*100000
+
+variable	gravity equal 1.0
+variable	density equal 1.0
+
+variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable	a equal (-2.0*log(${coeffRes})/PI)^2
+variable	a equal (-2.0*log(0.1)/PI)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 806.699778405191*0.5
+
+variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable	dt equal ${tcol}*0.02
+variable	dt equal 0.00236257621510454*0.02
+timestep	${dt}
+timestep	4.72515243020908e-05
+
+###############################################
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		on
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block 0 20 0 20 0 20
+create_box	1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.6 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0
+  ghost atom cutoff = 0
+  binsize = 20, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/multi/newton
+      stencil: half/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region	     	insreg cylinder z 10 10 8 10 18 side in units box
+region	    	cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable	theta equal (step/400000)*2*PI
+
+region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
+region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
+
+region		mixer intersect 3 cylreg b1 b2 side in
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+
+#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:896)
+thermo_modify	flush yes lost warn
+
+run		200000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+         0   0                      0  -0              0            
+      1000   0.10672296           444  -0              0.015707963  
+      2000   0.2090638            444  -0              0.031415927  
+      3000   0.31029663           444  -0              0.04712389   
+      4000   0.41047624           444  -0              0.062831853  
+      5000   0.51132361           444  -0              0.078539816  
+      6000   0.61279172           444  -0              0.09424778   
+      7000   0.71396622           444  -0              0.10995574   
+      8000   0.81644319           444  -0              0.12566371   
+      9000   0.91730959           444  -0              0.14137167   
+     10000   1.0181635            444  -0              0.15707963   
+     11000   1.1182214            444  -0              0.1727876    
+     12000   1.2190013            444  -0              0.18849556   
+     13000   1.3196138            444  -0              0.20420352   
+     14000   1.4183593            444  -0              0.21991149   
+     15000   1.5178458            444  -0              0.23561945   
+     16000   1.6169535            444  -0              0.25132741   
+     17000   1.7219188            444  -0              0.26703538   
+     18000   1.8266303            444  -0              0.28274334   
+     19000   1.9331589            444  -0              0.2984513    
+     20000   2.0392693            444  -0              0.31415927   
+     21000   2.1457521            444  -0              0.32986723   
+     22000   2.2507526            444  -0              0.34557519   
+     23000   2.3548243            444  -0              0.36128316   
+     24000   2.4606335            444  -0              0.37699112   
+     25000   2.5657643            444  -0              0.39269908   
+     26000   2.6698254            444  -0              0.40840704   
+     27000   2.7732221            444  -0              0.42411501   
+     28000   2.8766441            444  -0              0.43982297   
+     29000   2.9801547            444  -0              0.45553093   
+     30000   3.0839748            444  -0              0.4712389    
+     31000   3.1880063            444  -0              0.48694686   
+     32000   3.2923439            444  -0              0.50265482   
+     33000   3.3969501            444  -0              0.51836279   
+     34000   3.5012646            444  -0              0.53407075   
+     35000   3.6057831            444  -0              0.54977871   
+     36000   3.7098273            444  -0              0.56548668   
+     37000   3.8146061            444  -0              0.58119464   
+     38000   3.9215588            444  -0              0.5969026    
+     39000   4.0474026            444  -0              0.61261057   
+     40000   4.1544945            444  -0              0.62831853   
+     41000   4.2605761            444  -0              0.64402649   
+     42000   4.3665287            444  -0              0.65973446   
+     43000   4.4728216            444  -0              0.67544242   
+     44000   4.5782483            444  -0              0.69115038   
+     45000   4.6833043            444  -0              0.70685835   
+     46000   4.7902207            444  -0              0.72256631   
+     47000   4.8968527            444  -0              0.73827427   
+     48000   5.0035027            444  -0              0.75398224   
+     49000   5.1117191            444  -0              0.7696902    
+     50000   5.2186233            444  -0              0.78539816   
+     51000   5.3244005            444  -0              0.80110613   
+     52000   5.4316153            444  -0              0.81681409   
+     53000   5.5381785            444  -0              0.83252205   
+     54000   5.6458179            444  -0              0.84823002   
+     55000   5.759203             444  -0              0.86393798   
+     56000   5.8779849            444  -0              0.87964594   
+     57000   5.9953108            444  -0              0.89535391   
+     58000   6.1115532            444  -0              0.91106187   
+     59000   6.2298342            444  -0              0.92676983   
+     60000   6.3474382            444  -0              0.9424778    
+     61000   6.4642217            444  -0              0.95818576   
+     62000   6.5815141            444  -0              0.97389372   
+     63000   6.6999766            444  -0              0.98960169   
+     64000   6.8181369            444  -0              1.0053096    
+     65000   6.9368124            444  -0              1.0210176    
+     66000   7.0560733            444  -0              1.0367256    
+     67000   7.1761749            444  -0              1.0524335    
+     68000   7.2942246            444  -0              1.0681415    
+     69000   7.4146786            444  -0              1.0838495    
+     70000   7.5364025            444  -0              1.0995574    
+     71000   7.6565177            444  -0              1.1152654    
+     72000   7.7776652            444  -0              1.1309734    
+     73000   7.8972494            444  -0              1.1466813    
+     74000   8.0183599            444  -0              1.1623893    
+     75000   8.1423045            444  -0              1.1780972    
+     76000   8.2667013            444  -0              1.1938052    
+     77000   8.3876604            444  -0              1.2095132    
+     78000   8.5095993            444  -0              1.2252211    
+     79000   8.6317663            444  -0              1.2409291    
+     80000   8.7562108            444  -0              1.2566371    
+     81000   8.8812625            444  -0              1.272345     
+     82000   9.006825             444  -0              1.288053     
+     83000   9.1310939            444  -0              1.303761     
+     84000   9.2540049            444  -0              1.3194689    
+     85000   9.4210019            888  -0              1.3351769    
+     86000   9.6509014            888  -0              1.3508848    
+     87000   9.8827304            888  -0              1.3665928    
+     88000   10.113857            888  -0              1.3823008    
+     89000   10.34324             888  -0              1.3980087    
+     90000   10.574203            888  -0              1.4137167    
+     91000   10.806069            888  -0              1.4294247    
+     92000   11.037044            888  -0              1.4451326    
+     93000   11.262596            888  -0              1.4608406    
+     94000   11.490532            888  -0              1.4765485    
+     95000   11.716452            888  -0              1.4922565    
+     96000   11.943883            888  -0              1.5079645    
+     97000   12.171353            888  -0              1.5236724    
+     98000   12.396787            888  -0              1.5393804    
+     99000   12.623788            888  -0              1.5550884    
+    100000   12.849633            888  -0              1.5707963    
+    101000   13.082904            888  -0              1.5865043    
+    102000   13.316986            888  -0              1.6022123    
+    103000   13.54777             888  -0              1.6179202    
+    104000   13.77928             888  -0              1.6336282    
+    105000   14.014818            888  -0              1.6493361    
+    106000   14.250986            888  -0              1.6650441    
+    107000   14.485754            888  -0              1.6807521    
+    108000   14.720106            888  -0              1.69646      
+    109000   14.970869            888  -0              1.712168     
+    110000   15.219203            888  -0              1.727876     
+    111000   15.469876            888  -0              1.7435839    
+    112000   15.721351            888  -0              1.7592919    
+    113000   15.972099            888  -0              1.7749998    
+    114000   16.222357            888  -0              1.7907078    
+    115000   16.474863            888  -0              1.8064158    
+    116000   16.725352            888  -0              1.8221237    
+    117000   16.979634            888  -0              1.8378317    
+    118000   17.231379            888  -0              1.8535397    
+    119000   17.483691            888  -0              1.8692476    
+    120000   17.737897            888  -0              1.8849556    
+    121000   17.991241            888  -0              1.9006636    
+    122000   18.245626            888  -0              1.9163715    
+    123000   18.499984            888  -0              1.9320795    
+    124000   18.754367            888  -0              1.9477874    
+    125000   19.006448            888  -0              1.9634954    
+    126000   19.260545            888  -0              1.9792034    
+    127000   19.513633            888  -0              1.9949113    
+    128000   19.769389            888  -0              2.0106193    
+    129000   20.025088            888  -0              2.0263273    
+    130000   20.277534            888  -0              2.0420352    
+    131000   20.529284            888  -0              2.0577432    
+    132000   20.785132            888  -0              2.0734512    
+    133000   21.038442            888  -0              2.0891591    
+    134000   21.293932            888  -0              2.1048671    
+    135000   21.545354            888  -0              2.120575     
+    136000   21.799547            888  -0              2.136283     
+    137000   22.053639            888  -0              2.151991     
+    138000   22.310106            888  -0              2.1676989    
+    139000   22.569362            888  -0              2.1834069    
+    140000   22.829416            888  -0              2.1991149    
+    141000   23.089132            888  -0              2.2148228    
+    142000   23.345737            888  -0              2.2305308    
+    143000   23.60621             888  -0              2.2462387    
+    144000   23.867414            888  -0              2.2619467    
+    145000   24.132954            888  -0              2.2776547    
+    146000   24.39395             888  -0              2.2933626    
+    147000   24.657881            888  -0              2.3090706    
+    148000   24.918563            888  -0              2.3247786    
+    149000   25.177446            888  -0              2.3404865    
+    150000   25.446598            888  -0              2.3561945    
+    151000   25.715494            888  -0              2.3719025    
+    152000   25.985991            888  -0              2.3876104    
+    153000   26.256676            888  -0              2.4033184    
+    154000   26.525639            888  -0              2.4190263    
+    155000   26.82656             888  -0              2.4347343    
+    156000   27.157272            888  -0              2.4504423    
+    157000   27.481755            888  -0              2.4661502    
+    158000   27.80198             888  -0              2.4818582    
+    159000   28.123258            888  -0              2.4975662    
+    160000   28.437502            888  -0              2.5132741    
+    161000   28.756496            888  -0              2.5289821    
+    162000   29.080609            888  -0              2.54469      
+    163000   29.399252            888  -0              2.560398     
+    164000   29.718986            888  -0              2.576106     
+    165000   30.045206            888  -0              2.5918139    
+    166000   30.365168            888  -0              2.6075219    
+    167000   30.684007            888  -0              2.6232299    
+    168000   31.006154            888  -0              2.6389378    
+    169000   31.330336            888  -0              2.6546458    
+    170000   31.681761           1000  -0              2.6703538    
+    171000   32.049778           1000  -0              2.6860617    
+    172000   32.421067           1000  -0              2.7017697    
+    173000   32.79935            1000  -0              2.7174776    
+    174000   33.178002           1000  -0              2.7331856    
+    175000   33.54236            1000  -0              2.7488936    
+    176000   33.904734           1000  -0              2.7646015    
+    177000   34.269671           1000  -0              2.7803095    
+    178000   34.633106           1000  -0              2.7960175    
+    179000   35.001441           1000  -0              2.8117254    
+    180000   35.374769           1000  -0              2.8274334    
+    181000   35.742362           1000  -0              2.8431414    
+    182000   36.115908           1000  -0              2.8588493    
+    183000   36.490149           1000  -0              2.8745573    
+    184000   36.866289           1000  -0              2.8902652    
+    185000   37.252911           1000  -0              2.9059732    
+    186000   37.644586           1000  -0              2.9216812    
+    187000   38.028002           1000  -0              2.9373891    
+    188000   38.40724            1000  -0              2.9530971    
+    189000   38.77431            1000  -0              2.9688051    
+    190000   39.14138            1000  -0              2.984513     
+    191000   39.519083           1000  -0              3.000221     
+    192000   39.895243           1000  -0              3.0159289    
+    193000   40.237532           1000  -0              3.0316369    
+    194000   40.587663           1000  -0              3.0473449    
+    195000   40.939032           1000  -0              3.0630528    
+    196000   41.290257           1000  -0              3.0787608    
+    197000   41.643778           1000  -0              3.0944688    
+    198000   41.992818           1000  -0              3.1101767    
+    199000   42.335934           1000  -0              3.1258847    
+    200000   42.681071           1000  -0              3.1415927    
+Loop time of 42.6811 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 19130.397 tau/day, 4685.915 timesteps/s, 4.686 Matom-step/s
+98.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.6365     | 2.6365     | 2.6365     |   0.0 |  6.18
+Neigh   | 0.051681   | 0.051681   | 0.051681   |   0.0 |  0.12
+Comm    | 0.52007    | 0.52007    | 0.52007    |   0.0 |  1.22
+Output  | 0.02209    | 0.02209    | 0.02209    |   0.0 |  0.05
+Modify  | 38.71      | 38.71      | 38.71      |   0.0 | 90.70
+Other   |            | 0.7407     |            |       |  1.74
+
+Nlocal:           1000 ave        1000 max        1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            183 ave         183 max         183 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           3757 ave        3757 max        3757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3757
+Ave neighs/atom = 3.757
+Neighbor list builds = 200
+Dangerous builds = 0
+unfix 		ins
+run		200000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+    200000   0                   1000   1.0515941      3.1415927    
+    201000   0.35477257          1000   1.0348185      3.1573006    
+    202000   0.71436123          1000   1.0220859      3.1730086    
+    203000   1.0642832           1000   1.0225785      3.1887165    
+    204000   1.4165213           1000   1.0206121      3.2044245    
+    205000   1.7728133           1000   1.009961       3.2201325    
+    206000   2.1279101           1000   0.9993323      3.2358404    
+    207000   2.480623            1000   0.99602628     3.2515484    
+    208000   2.8321106           1000   0.98341818     3.2672564    
+    209000   3.2138945           1000   0.96700718     3.2829643    
+    210000   3.5921146           1000   0.95226699     3.2986723    
+    211000   3.9643569           1000   0.93911691     3.3143802    
+    212000   4.3368151           1000   0.92920029     3.3300882    
+    213000   4.7130192           1000   0.91893472     3.3457962    
+    214000   5.0881313           1000   0.90873324     3.3615041    
+    215000   5.4660106           1000   0.88925817     3.3772121    
+    216000   5.8455926           1000   0.89108236     3.3929201    
+    217000   6.2204827           1000   0.90176711     3.408628     
+    218000   6.6046736           1000   0.90149435     3.424336     
+    219000   6.9931145           1000   0.89629307     3.440044     
+    220000   7.3771565           1000   0.90390589     3.4557519    
+    221000   7.7635603           1000   0.87858148     3.4714599    
+    222000   8.1502771           1000   0.88862314     3.4871678    
+    223000   8.5393557           1000   0.90394098     3.5028758    
+    224000   8.9327212           1000   0.91005462     3.5185838    
+    225000   9.315331            1000   0.91753865     3.5342917    
+    226000   9.6930994           1000   0.91741233     3.5499997    
+    227000   10.077148           1000   0.9041879      3.5657077    
+    228000   10.463223           1000   0.9085712      3.5814156    
+    229000   10.850271           1000   0.8937854      3.5971236    
+    230000   11.230235           1000   0.88740571     3.6128316    
+    231000   11.61003            1000   0.88350028     3.6285395    
+    232000   11.988134           1000   0.88344474     3.6442475    
+    233000   12.365856           1000   0.88003311     3.6599554    
+    234000   12.745397           1000   0.87416727     3.6756634    
+    235000   13.120344           1000   0.86154585     3.6913714    
+    236000   13.489521           1000   0.85705071     3.7070793    
+    237000   13.858736           1000   0.85297378     3.7227873    
+    238000   14.230242           1000   0.84879486     3.7384953    
+    239000   14.609692           1000   0.86978407     3.7542032    
+    240000   14.998899           1000   0.86758733     3.7699112    
+    241000   15.40773            1000   0.86123097     3.7856191    
+    242000   15.81537            1000   0.86088136     3.8013271    
+    243000   16.221448           1000   0.85270311     3.8170351    
+    244000   16.619008           1000   0.8524395      3.832743     
+    245000   17.003986           1000   0.84054009     3.848451     
+    246000   17.380362           1000   0.82623612     3.864159     
+    247000   17.756477           1000   0.82787746     3.8798669    
+    248000   18.136456           1000   0.83027177     3.8955749    
+    249000   18.521277           1000   0.83307565     3.9112829    
+    250000   18.906407           1000   0.82612362     3.9269908    
+    251000   19.28348            1000   0.8404639      3.9426988    
+    252000   19.66549            1000   0.83550946     3.9584067    
+    253000   20.053842           1000   0.81516472     3.9741147    
+    254000   20.451357           1000   0.79127421     3.9898227    
+    255000   20.844416           1000   0.78373024     4.0055306    
+    256000   21.228637           1000   0.79885661     4.0212386    
+    257000   21.613641           1000   0.80322118     4.0369466    
+    258000   21.99162            1000   0.79861523     4.0526545    
+    259000   22.367158           1000   0.79216962     4.0683625    
+    260000   22.746158           1000   0.79543097     4.0840704    
+    261000   23.125626           1000   0.79394211     4.0997784    
+    262000   23.504282           1000   0.79269346     4.1154864    
+    263000   23.883609           1000   0.80022854     4.1311943    
+    264000   24.261864           1000   0.79885184     4.1469023    
+    265000   24.639269           1000   0.79595018     4.1626103    
+    266000   25.016335           1000   0.78191184     4.1783182    
+    267000   25.389754           1000   0.76329279     4.1940262    
+    268000   25.762053           1000   0.7342663      4.2097342    
+    269000   26.133966           1000   0.72303366     4.2254421    
+    270000   26.511157           1000   0.70016481     4.2411501    
+    271000   26.888842           1000   0.68891731     4.256858     
+    272000   27.26804            1000   0.68545775     4.272566     
+    273000   27.644067           1000   0.68712156     4.288274     
+    274000   28.024704           1000   0.69249813     4.3039819    
+    275000   28.404842           1000   0.70187847     4.3196899    
+    276000   28.785799           1000   0.70679419     4.3353979    
+    277000   29.165857           1000   0.70955357     4.3511058    
+    278000   29.545291           1000   0.70183408     4.3668138    
+    279000   29.926113           1000   0.69979273     4.3825218    
+    280000   30.302095           1000   0.70822139     4.3982297    
+    281000   30.684406           1000   0.71629209     4.4139377    
+    282000   31.065873           1000   0.73094905     4.4296456    
+    283000   31.445972           1000   0.74554115     4.4453536    
+    284000   31.828184           1000   0.74390104     4.4610616    
+    285000   32.207807           1000   0.74675359     4.4767695    
+    286000   32.58802            1000   0.75330713     4.4924775    
+    287000   32.964457           1000   0.75525926     4.5081855    
+    288000   33.343222           1000   0.75174884     4.5238934    
+    289000   33.717663           1000   0.74062375     4.5396014    
+    290000   34.094722           1000   0.72784613     4.5553093    
+    291000   34.46982            1000   0.72151574     4.5710173    
+    292000   34.843777           1000   0.71712409     4.5867253    
+    293000   35.208307           1000   0.71803758     4.6024332    
+    294000   35.576207           1000   0.71002715     4.6181412    
+    295000   35.942972           1000   0.7070911      4.6338492    
+    296000   36.3107             1000   0.71082175     4.6495571    
+    297000   36.682044           1000   0.70438977     4.6652651    
+    298000   37.054664           1000   0.70240345     4.6809731    
+    299000   37.424717           1000   0.70525357     4.696681     
+    300000   37.796148           1000   0.70636846     4.712389     
+    301000   38.166828           1000   0.70443346     4.7280969    
+    302000   38.538428           1000   0.71187973     4.7438049    
+    303000   38.907221           1000   0.71047139     4.7595129    
+    304000   39.280263           1000   0.71405925     4.7752208    
+    305000   39.652902           1000   0.71277063     4.7909288    
+    306000   40.02752            1000   0.72005331     4.8066368    
+    307000   40.402955           1000   0.72466112     4.8223447    
+    308000   40.784177           1000   0.72001329     4.8380527    
+    309000   41.173226           1000   0.70611982     4.8537606    
+    310000   41.559195           1000   0.70810918     4.8694686    
+    311000   41.946697           1000   0.70377166     4.8851766    
+    312000   42.337059           1000   0.70434458     4.9008845    
+    313000   42.728304           1000   0.70707385     4.9165925    
+    314000   43.120803           1000   0.71412995     4.9323005    
+    315000   43.510705           1000   0.72228946     4.9480084    
+    316000   43.901867           1000   0.72715835     4.9637164    
+    317000   44.295667           1000   0.73833476     4.9794244    
+    318000   44.687503           1000   0.75953014     4.9951323    
+    319000   45.077121           1000   0.76413836     5.0108403    
+    320000   45.465317           1000   0.76745045     5.0265482    
+    321000   45.86931            1000   0.75813288     5.0422562    
+    322000   46.277029           1000   0.75324661     5.0579642    
+    323000   46.680799           1000   0.75004276     5.0736721    
+    324000   47.082361           1000   0.74316264     5.0893801    
+    325000   47.481252           1000   0.74087383     5.1050881    
+    326000   47.87511            1000   0.73244882     5.120796     
+    327000   48.274582           1000   0.73096631     5.136504     
+    328000   48.671718           1000   0.72955403     5.152212     
+    329000   49.066335           1000   0.73464916     5.1679199    
+    330000   49.459765           1000   0.73130257     5.1836279    
+    331000   49.850698           1000   0.73008711     5.1993358    
+    332000   50.241012           1000   0.72561074     5.2150438    
+    333000   50.643245           1000   0.7214495      5.2307518    
+    334000   51.039153           1000   0.71274232     5.2464597    
+    335000   51.430328           1000   0.71335777     5.2621677    
+    336000   51.819148           1000   0.71317423     5.2778757    
+    337000   52.202763           1000   0.70965743     5.2935836    
+    338000   52.585061           1000   0.69648518     5.3092916    
+    339000   52.967678           1000   0.68985842     5.3249995    
+    340000   53.351472           1000   0.6846783      5.3407075    
+    341000   53.737731           1000   0.69031602     5.3564155    
+    342000   54.131413           1000   0.69035259     5.3721234    
+    343000   54.526384           1000   0.69843983     5.3878314    
+    344000   54.921609           1000   0.69566088     5.4035394    
+    345000   55.314258           1000   0.68309182     5.4192473    
+    346000   55.701119           1000   0.68360919     5.4349553    
+    347000   56.088194           1000   0.68034628     5.4506633    
+    348000   56.467878           1000   0.67155093     5.4663712    
+    349000   56.857709           1000   0.66504603     5.4820792    
+    350000   57.250758           1000   0.66533658     5.4977871    
+    351000   57.643438           1000   0.67726804     5.5134951    
+    352000   58.04256            1000   0.68880987     5.5292031    
+    353000   58.437369           1000   0.71377276     5.544911     
+    354000   58.832421           1000   0.71715625     5.560619     
+    355000   59.222221           1000   0.71729576     5.576327     
+    356000   59.621431           1000   0.71088872     5.5920349    
+    357000   60.013262           1000   0.70564615     5.6077429    
+    358000   60.406494           1000   0.69291739     5.6234508    
+    359000   60.800632           1000   0.68237469     5.6391588    
+    360000   61.195364           1000   0.69105856     5.6548668    
+    361000   61.588291           1000   0.69563351     5.6705747    
+    362000   61.984821           1000   0.69762747     5.6862827    
+    363000   62.377158           1000   0.69717346     5.7019907    
+    364000   62.77604            1000   0.69413964     5.7176986    
+    365000   63.165863           1000   0.68584257     5.7334066    
+    366000   63.5503             1000   0.67653762     5.7491146    
+    367000   63.930717           1000   0.66880284     5.7648225    
+    368000   64.313698           1000   0.66024732     5.7805305    
+    369000   64.708193           1000   0.65451701     5.7962384    
+    370000   65.10142            1000   0.64352268     5.8119464    
+    371000   65.49169            1000   0.63715296     5.8276544    
+    372000   65.879115           1000   0.63840106     5.8433623    
+    373000   66.268258           1000   0.64537192     5.8590703    
+    374000   66.661807           1000   0.64498753     5.8747783    
+    375000   67.052521           1000   0.64666103     5.8904862    
+    376000   67.443168           1000   0.65957055     5.9061942    
+    377000   67.835892           1000   0.65964257     5.9219022    
+    378000   68.229282           1000   0.65720396     5.9376101    
+    379000   68.623557           1000   0.66304265     5.9533181    
+    380000   69.015967           1000   0.67465814     5.969026     
+    381000   69.408981           1000   0.68582945     5.984734     
+    382000   69.796561           1000   0.69516677     6.000442     
+    383000   70.186403           1000   0.69835516     6.0161499    
+    384000   70.5765             1000   0.70403284     6.0318579    
+    385000   70.966205           1000   0.6955862      6.0475659    
+    386000   71.360054           1000   0.704932       6.0632738    
+    387000   71.757912           1000   0.71954173     6.0789818    
+    388000   72.147544           1000   0.72347529     6.0946897    
+    389000   72.535029           1000   0.72738907     6.1103977    
+    390000   72.925842           1000   0.74783091     6.1261057    
+    391000   73.306871           1000   0.76739039     6.1418136    
+    392000   73.692746           1000   0.77184224     6.1575216    
+    393000   74.053385           1000   0.76813357     6.1732296    
+    394000   74.416323           1000   0.75994091     6.1889375    
+    395000   74.777021           1000   0.74970188     6.2046455    
+    396000   75.139847           1000   0.7523174      6.2203535    
+    397000   75.502888           1000   0.74652931     6.2360614    
+    398000   75.865442           1000   0.74418096     6.2517694    
+    399000   76.225245           1000   0.75110038     6.2674773    
+    400000   76.590032           1000   0.7609274      6.2831853    
+Loop time of 76.5901 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 10660.735 tau/day, 2611.305 timesteps/s, 2.611 Matom-step/s
+99.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.693      | 8.693      | 8.693      |   0.0 | 11.35
+Neigh   | 0.082655   | 0.082655   | 0.082655   |   0.0 |  0.11
+Comm    | 1.1618     | 1.1618     | 1.1618     |   0.0 |  1.52
+Output  | 0.0052644  | 0.0052644  | 0.0052644  |   0.0 |  0.01
+Modify  | 65.713     | 65.713     | 65.713     |   0.0 | 85.80
+Other   |            | 0.934      |            |       |  1.22
+
+Nlocal:           1000 ave        1000 max        1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            268 ave         268 max         268 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           5015 ave        5015 max        5015 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5015
+Ave neighs/atom = 5.015
+Neighbor list builds = 163
+Dangerous builds = 0
+Total wall time: 0:01:59

examples/granregion/log.15Sep22.granregion.mixer.g++.4

@@ -0,0 +1,632 @@
+LAMMPS (15 Sep 2022)
+variable	name string mixer
+
+thermo_modify	flush yes
+variable	seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable	rlo equal 0.3
+variable	rhi equal 0.6
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.3
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.6
+variable 	skin equal ${rhi}
+variable 	skin equal 0.6
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	kn equal 10^5
+variable	kt equal 0.2*${kn}
+variable	kt equal 0.2*100000
+
+variable	gravity equal 1.0
+variable	density equal 1.0
+
+variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable	a equal (-2.0*log(${coeffRes})/PI)^2
+variable	a equal (-2.0*log(0.1)/PI)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 806.699778405191*0.5
+
+variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable	dt equal ${tcol}*0.02
+variable	dt equal 0.00236257621510454*0.02
+timestep	${dt}
+timestep	4.72515243020908e-05
+
+###############################################
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		on
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block 0 20 0 20 0 20
+create_box	1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.6 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0
+  ghost atom cutoff = 0
+  binsize = 20, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/multi/newton
+      stencil: half/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region	     	insreg cylinder z 10 10 8 10 18 side in units box
+region	    	cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable	theta equal (step/400000)*2*PI
+
+region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
+region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
+
+region		mixer intersect 3 cylreg b1 b2 side in
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+
+#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:896)
+thermo_modify	flush yes lost warn
+
+run		200000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+         0   0                      0  -0              0            
+      1000   0.089993907          444  -0              0.015707963  
+      2000   0.14885989           444  -0              0.031415927  
+      3000   0.20954563           444  -0              0.04712389   
+      4000   0.27002257           444  -0              0.062831853  
+      5000   0.33034347           444  -0              0.078539816  
+      6000   0.39049526           444  -0              0.09424778   
+      7000   0.45002664           444  -0              0.10995574   
+      8000   0.50911338           444  -0              0.12566371   
+      9000   0.56771745           444  -0              0.14137167   
+     10000   0.62699472           444  -0              0.15707963   
+     11000   0.67300351           444  -0              0.1727876    
+     12000   0.71981356           444  -0              0.18849556   
+     13000   0.76697682           444  -0              0.20420352   
+     14000   0.81412229           444  -0              0.21991149   
+     15000   0.86284749           444  -0              0.23561945   
+     16000   0.91199522           444  -0              0.25132741   
+     17000   0.96230663           444  -0              0.26703538   
+     18000   1.0118327            444  -0              0.28274334   
+     19000   1.0617397            444  -0              0.2984513    
+     20000   1.111586             444  -0              0.31415927   
+     21000   1.1556637            444  -0              0.32986723   
+     22000   1.2005913            444  -0              0.34557519   
+     23000   1.2455061            444  -0              0.36128316   
+     24000   1.2910181            444  -0              0.37699112   
+     25000   1.3370577            444  -0              0.39269908   
+     26000   1.383595             444  -0              0.40840704   
+     27000   1.430922             444  -0              0.42411501   
+     28000   1.478627             444  -0              0.43982297   
+     29000   1.5278607            444  -0              0.45553093   
+     30000   1.576597             444  -0              0.4712389    
+     31000   1.6202694            444  -0              0.48694686   
+     32000   1.6646667            444  -0              0.50265482   
+     33000   1.7092726            444  -0              0.51836279   
+     34000   1.7535573            444  -0              0.53407075   
+     35000   1.7985995            444  -0              0.54977871   
+     36000   1.8440346            444  -0              0.56548668   
+     37000   1.8900841            444  -0              0.58119464   
+     38000   1.9368772            444  -0              0.5969026    
+     39000   1.9842867            444  -0              0.61261057   
+     40000   2.0318482            444  -0              0.62831853   
+     41000   2.0753049            444  -0              0.64402649   
+     42000   2.1196274            444  -0              0.65973446   
+     43000   2.1647071            444  -0              0.67544242   
+     44000   2.2101195            444  -0              0.69115038   
+     45000   2.2564642            444  -0              0.70685835   
+     46000   2.3033573            444  -0              0.72256631   
+     47000   2.3500515            444  -0              0.73827427   
+     48000   2.3972268            444  -0              0.75398224   
+     49000   2.4444727            444  -0              0.7696902    
+     50000   2.4921003            444  -0              0.78539816   
+     51000   2.535088             444  -0              0.80110613   
+     52000   2.5785564            444  -0              0.81681409   
+     53000   2.6221392            444  -0              0.83252205   
+     54000   2.6664169            444  -0              0.84823002   
+     55000   2.7108951            444  -0              0.86393798   
+     56000   2.7560522            444  -0              0.87964594   
+     57000   2.8010254            444  -0              0.89535391   
+     58000   2.8484456            444  -0              0.91106187   
+     59000   2.8951674            444  -0              0.92676983   
+     60000   2.9424205            444  -0              0.9424778    
+     61000   2.9885999            444  -0              0.95818576   
+     62000   3.0338676            444  -0              0.97389372   
+     63000   3.0793674            444  -0              0.98960169   
+     64000   3.1253557            444  -0              1.0053096    
+     65000   3.1723823            444  -0              1.0210176    
+     66000   3.2203846            444  -0              1.0367256    
+     67000   3.2690443            444  -0              1.0524335    
+     68000   3.317707             444  -0              1.0681415    
+     69000   3.3670196            444  -0              1.0838495    
+     70000   3.4160505            444  -0              1.0995574    
+     71000   3.4621197            444  -0              1.1152654    
+     72000   3.5086434            444  -0              1.1309734    
+     73000   3.555691             444  -0              1.1466813    
+     74000   3.6032072            444  -0              1.1623893    
+     75000   3.6514849            444  -0              1.1780972    
+     76000   3.7002713            444  -0              1.1938052    
+     77000   3.7497321            444  -0              1.2095132    
+     78000   3.7997711            444  -0              1.2252211    
+     79000   3.8504338            444  -0              1.2409291    
+     80000   3.9020416            444  -0              1.2566371    
+     81000   3.9496762            444  -0              1.272345     
+     82000   3.9968215            444  -0              1.288053     
+     83000   4.04496              444  -0              1.303761     
+     84000   4.0936477            444  -0              1.3194689    
+     85000   4.1618384            888  -0              1.3351769    
+     86000   4.2472086            888  -0              1.3508848    
+     87000   4.3322855            888  -0              1.3665928    
+     88000   4.4169835            888  -0              1.3823008    
+     89000   4.5014588            888  -0              1.3980087    
+     90000   4.5861842            888  -0              1.4137167    
+     91000   4.653654             888  -0              1.4294247    
+     92000   4.7217642            888  -0              1.4451326    
+     93000   4.791842             888  -0              1.4608406    
+     94000   4.8601789            888  -0              1.4765485    
+     95000   4.92849              888  -0              1.4922565    
+     96000   4.9976811            888  -0              1.5079645    
+     97000   5.0687073            888  -0              1.5236724    
+     98000   5.1387234            888  -0              1.5393804    
+     99000   5.2086037            888  -0              1.5550884    
+    100000   5.2786924            888  -0              1.5707963    
+    101000   5.3466895            888  -0              1.5865043    
+    102000   5.417132             888  -0              1.6022123    
+    103000   5.4865633            888  -0              1.6179202    
+    104000   5.5565911            888  -0              1.6336282    
+    105000   5.6266394            888  -0              1.6493361    
+    106000   5.6975394            888  -0              1.6650441    
+    107000   5.7687753            888  -0              1.6807521    
+    108000   5.8408498            888  -0              1.69646      
+    109000   5.9132618            888  -0              1.712168     
+    110000   5.9872629            888  -0              1.727876     
+    111000   6.0588115            888  -0              1.7435839    
+    112000   6.1308729            888  -0              1.7592919    
+    113000   6.2047311            888  -0              1.7749998    
+    114000   6.2780757            888  -0              1.7907078    
+    115000   6.3528542            888  -0              1.8064158    
+    116000   6.4277704            888  -0              1.8221237    
+    117000   6.5034683            888  -0              1.8378317    
+    118000   6.5795779            888  -0              1.8535397    
+    119000   6.655928             888  -0              1.8692476    
+    120000   6.7335119            888  -0              1.8849556    
+    121000   6.806827             888  -0              1.9006636    
+    122000   6.881052             888  -0              1.9163715    
+    123000   6.9559647            888  -0              1.9320795    
+    124000   7.0300829            888  -0              1.9477874    
+    125000   7.1047925            888  -0              1.9634954    
+    126000   7.1797025            888  -0              1.9792034    
+    127000   7.2556934            888  -0              1.9949113    
+    128000   7.3317803            888  -0              2.0106193    
+    129000   7.4088096            888  -0              2.0263273    
+    130000   7.4862461            888  -0              2.0420352    
+    131000   7.5633585            888  -0              2.0577432    
+    132000   7.641939             888  -0              2.0734512    
+    133000   7.7192741            888  -0              2.0891591    
+    134000   7.7970156            888  -0              2.1048671    
+    135000   7.8760712            888  -0              2.120575     
+    136000   7.9563099            888  -0              2.136283     
+    137000   8.0381808            888  -0              2.151991     
+    138000   8.1210957            888  -0              2.1676989    
+    139000   8.20401              888  -0              2.1834069    
+    140000   8.2871705            888  -0              2.1991149    
+    141000   8.364321             888  -0              2.2148228    
+    142000   8.4426744            888  -0              2.2305308    
+    143000   8.5238377            888  -0              2.2462387    
+    144000   8.6050517            888  -0              2.2619467    
+    145000   8.6865872            888  -0              2.2776547    
+    146000   8.767621             888  -0              2.2933626    
+    147000   8.8496616            888  -0              2.3090706    
+    148000   8.9329599            888  -0              2.3247786    
+    149000   9.0165929            888  -0              2.3404865    
+    150000   9.1015214            888  -0              2.3561945    
+    151000   9.1847289            888  -0              2.3719025    
+    152000   9.2689185            888  -0              2.3876104    
+    153000   9.3518862            888  -0              2.4033184    
+    154000   9.4367057            888  -0              2.4190263    
+    155000   9.5227466            888  -0              2.4347343    
+    156000   9.6087196            888  -0              2.4504423    
+    157000   9.6955661            888  -0              2.4661502    
+    158000   9.7838227            888  -0              2.4818582    
+    159000   9.8731804            888  -0              2.4975662    
+    160000   9.9626648            888  -0              2.5132741    
+    161000   10.050473            888  -0              2.5289821    
+    162000   10.137725            888  -0              2.54469      
+    163000   10.227259            888  -0              2.560398     
+    164000   10.318501            888  -0              2.576106     
+    165000   10.409218            888  -0              2.5918139    
+    166000   10.502055            888  -0              2.6075219    
+    167000   10.593786            888  -0              2.6232299    
+    168000   10.688536            888  -0              2.6389378    
+    169000   10.786033            888  -0              2.6546458    
+    170000   10.886377           1000  -0              2.6703538    
+    171000   10.987493           1000  -0              2.6860617    
+    172000   11.084584           1000  -0              2.7017697    
+    173000   11.181502           1000  -0              2.7174776    
+    174000   11.28434            1000  -0              2.7331856    
+    175000   11.387838           1000  -0              2.7488936    
+    176000   11.490915           1000  -0              2.7646015    
+    177000   11.595473           1000  -0              2.7803095    
+    178000   11.699823           1000  -0              2.7960175    
+    179000   11.803927           1000  -0              2.8117254    
+    180000   11.90548            1000  -0              2.8274334    
+    181000   12.00857            1000  -0              2.8431414    
+    182000   12.112787           1000  -0              2.8588493    
+    183000   12.217943           1000  -0              2.8745573    
+    184000   12.322668           1000  -0              2.8902652    
+    185000   12.428332           1000  -0              2.9059732    
+    186000   12.535414           1000  -0              2.9216812    
+    187000   12.642404           1000  -0              2.9373891    
+    188000   12.749332           1000  -0              2.9530971    
+    189000   12.856872           1000  -0              2.9688051    
+    190000   12.965335           1000  -0              2.984513     
+    191000   13.073275           1000  -0              3.000221     
+    192000   13.180122           1000  -0              3.0159289    
+    193000   13.288112           1000  -0              3.0316369    
+    194000   13.394688           1000  -0              3.0473449    
+    195000   13.501251           1000  -0              3.0630528    
+    196000   13.607472           1000  -0              3.0787608    
+    197000   13.71396            1000  -0              3.0944688    
+    198000   13.821133           1000  -0              3.1101767    
+    199000   13.929192           1000  -0              3.1258847    
+    200000   14.036724           1000  -0              3.1415927    
+Loop time of 14.0368 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 58169.166 tau/day, 14248.307 timesteps/s, 14.248 Matom-step/s
+95.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.47004    | 0.75698    | 1.1        |  33.1 |  5.39
+Neigh   | 0.0078501  | 0.010659   | 0.013902   |   2.7 |  0.08
+Comm    | 3.9589     | 4.4102     | 4.9322     |  21.6 | 31.42
+Output  | 0.0031054  | 0.0046208  | 0.0069341  |   2.1 |  0.03
+Modify  | 6.1829     | 6.8363     | 7.6135     |  24.8 | 48.70
+Other   |            | 2.018      |            |       | 14.38
+
+Nlocal:            250 ave         260 max         242 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost:         279.25 ave         325 max         232 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:         939.75 ave        1397 max         509 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3759
+Ave neighs/atom = 3.759
+Neighbor list builds = 201
+Dangerous builds = 0
+unfix 		ins
+run		200000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.88 | 11.89 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+    200000   0                   1000   1.0071568      3.1415927    
+    201000   0.099357585         1000   1.0036239      3.1573006    
+    202000   0.19922889          1000   0.99846844     3.1730086    
+    203000   0.29896537          1000   0.98236169     3.1887165    
+    204000   0.39875771          1000   0.98625572     3.2044245    
+    205000   0.49759454          1000   0.9893407      3.2201325    
+    206000   0.59609243          1000   1.0012123      3.2358404    
+    207000   0.69408206          1000   1.0231892      3.2515484    
+    208000   0.79216806          1000   1.0265912      3.2672564    
+    209000   0.8902274           1000   1.0190202      3.2829643    
+    210000   0.98909509          1000   1.0267754      3.2986723    
+    211000   1.0882901           1000   1.0186847      3.3143802    
+    212000   1.1895753           1000   1.0159848      3.3300882    
+    213000   1.2891277           1000   0.99326329     3.3457962    
+    214000   1.387486            1000   0.97263135     3.3615041    
+    215000   1.4850078           1000   0.97246409     3.3772121    
+    216000   1.58405             1000   0.96000626     3.3929201    
+    217000   1.6853829           1000   0.95730432     3.408628     
+    218000   1.7911163           1000   0.95605591     3.424336     
+    219000   1.8974141           1000   0.94983        3.440044     
+    220000   2.0029829           1000   0.95291888     3.4557519    
+    221000   2.108723            1000   0.93612997     3.4714599    
+    222000   2.2151561           1000   0.93414081     3.4871678    
+    223000   2.3220866           1000   0.93321246     3.5028758    
+    224000   2.4285504           1000   0.93026943     3.5185838    
+    225000   2.5356173           1000   0.930478       3.5342917    
+    226000   2.6415516           1000   0.92909096     3.5499997    
+    227000   2.747634            1000   0.92308495     3.5657077    
+    228000   2.8524082           1000   0.91075986     3.5814156    
+    229000   2.9570172           1000   0.9006662      3.5971236    
+    230000   3.0627535           1000   0.88869212     3.6128316    
+    231000   3.1683919           1000   0.8877611      3.6285395    
+    232000   3.2749534           1000   0.89409636     3.6442475    
+    233000   3.3824185           1000   0.90866091     3.6599554    
+    234000   3.4917899           1000   0.90454601     3.6756634    
+    235000   3.6009156           1000   0.89408327     3.6913714    
+    236000   3.7111309           1000   0.8881044      3.7070793    
+    237000   3.8197619           1000   0.89322168     3.7227873    
+    238000   3.9302291           1000   0.89018045     3.7384953    
+    239000   4.0407242           1000   0.88771268     3.7542032    
+    240000   4.1521989           1000   0.88957717     3.7699112    
+    241000   4.2639861           1000   0.89362036     3.7856191    
+    242000   4.3782856           1000   0.90967472     3.8013271    
+    243000   4.4925107           1000   0.91366381     3.8170351    
+    244000   4.6057342           1000   0.9150959      3.832743     
+    245000   4.7199383           1000   0.92725789     3.848451     
+    246000   4.8346784           1000   0.93024722     3.864159     
+    247000   4.9515438           1000   0.93297974     3.8798669    
+    248000   5.0696512           1000   0.94755869     3.8955749    
+    249000   5.1838845           1000   0.94761679     3.9112829    
+    250000   5.297991            1000   0.92701064     3.9269908    
+    251000   5.412562            1000   0.91365252     3.9426988    
+    252000   5.5274859           1000   0.90918381     3.9584067    
+    253000   5.6418647           1000   0.90612685     3.9741147    
+    254000   5.7593721           1000   0.90352142     3.9898227    
+    255000   5.8759086           1000   0.90421567     4.0055306    
+    256000   5.993588            1000   0.90024688     4.0212386    
+    257000   6.1142027           1000   0.88540341     4.0369466    
+    258000   6.2318882           1000   0.87890423     4.0526545    
+    259000   6.3502765           1000   0.86833748     4.0683625    
+    260000   6.4677878           1000   0.85465694     4.0840704    
+    261000   6.5875341           1000   0.83941242     4.0997784    
+    262000   6.7063481           1000   0.81790404     4.1154864    
+    263000   6.8249742           1000   0.82284562     4.1311943    
+    264000   6.9421188           1000   0.80961447     4.1469023    
+    265000   7.0588866           1000   0.80567073     4.1626103    
+    266000   7.1763855           1000   0.79577448     4.1783182    
+    267000   7.295632            1000   0.78489106     4.1940262    
+    268000   7.4144463           1000   0.77348757     4.2097342    
+    269000   7.5333839           1000   0.76606696     4.2254421    
+    270000   7.6527119           1000   0.7649744      4.2411501    
+    271000   7.7704222           1000   0.76050309     4.256858     
+    272000   7.8903012           1000   0.75378759     4.272566     
+    273000   8.0106197           1000   0.75633811     4.288274     
+    274000   8.1309707           1000   0.75703106     4.3039819    
+    275000   8.2522837           1000   0.75227453     4.3196899    
+    276000   8.3730898           1000   0.76003902     4.3353979    
+    277000   8.4955037           1000   0.76274661     4.3511058    
+    278000   8.6153206           1000   0.75888482     4.3668138    
+    279000   8.7339569           1000   0.75071875     4.3825218    
+    280000   8.8515447           1000   0.75454927     4.3982297    
+    281000   8.9685253           1000   0.75617824     4.4139377    
+    282000   9.0856168           1000   0.75230835     4.4296456    
+    283000   9.2018894           1000   0.75417571     4.4453536    
+    284000   9.3179777           1000   0.74559345     4.4610616    
+    285000   9.4341721           1000   0.73274661     4.4767695    
+    286000   9.5498722           1000   0.72385193     4.4924775    
+    287000   9.6651326           1000   0.72398899     4.5081855    
+    288000   9.7810274           1000   0.72009027     4.5238934    
+    289000   9.8959471           1000   0.72026686     4.5396014    
+    290000   10.010007           1000   0.72330145     4.5553093    
+    291000   10.123304           1000   0.71630656     4.5710173    
+    292000   10.238277           1000   0.71089192     4.5867253    
+    293000   10.351465           1000   0.70584923     4.6024332    
+    294000   10.464794           1000   0.71350398     4.6181412    
+    295000   10.57818            1000   0.72781836     4.6338492    
+    296000   10.692249           1000   0.72285512     4.6495571    
+    297000   10.80741            1000   0.71649517     4.6652651    
+    298000   10.923694           1000   0.71132209     4.6809731    
+    299000   11.039173           1000   0.73602072     4.696681     
+    300000   11.157002           1000   0.74400837     4.712389     
+    301000   11.272462           1000   0.76618562     4.7280969    
+    302000   11.386581           1000   0.77476041     4.7438049    
+    303000   11.499191           1000   0.77124283     4.7595129    
+    304000   11.611585           1000   0.7625748      4.7752208    
+    305000   11.725012           1000   0.74979361     4.7909288    
+    306000   11.838032           1000   0.74515733     4.8066368    
+    307000   11.949194           1000   0.74302741     4.8223447    
+    308000   12.060586           1000   0.73732959     4.8380527    
+    309000   12.171445           1000   0.73368237     4.8537606    
+    310000   12.283518           1000   0.72374292     4.8694686    
+    311000   12.393447           1000   0.72107784     4.8851766    
+    312000   12.505136           1000   0.72944426     4.9008845    
+    313000   12.616959           1000   0.73958637     4.9165925    
+    314000   12.730312           1000   0.75160847     4.9323005    
+    315000   12.846163           1000   0.74419683     4.9480084    
+    316000   12.960328           1000   0.74652593     4.9637164    
+    317000   13.073994           1000   0.74933482     4.9794244    
+    318000   13.186549           1000   0.74200509     4.9951323    
+    319000   13.296925           1000   0.7346024      5.0108403    
+    320000   13.406825           1000   0.72806145     5.0265482    
+    321000   13.51703            1000   0.72147888     5.0422562    
+    322000   13.628261           1000   0.71460041     5.0579642    
+    323000   13.74063            1000   0.70255075     5.0736721    
+    324000   13.853826           1000   0.70640327     5.0893801    
+    325000   13.968533           1000   0.70643428     5.1050881    
+    326000   14.081456           1000   0.69751794     5.120796     
+    327000   14.195505           1000   0.69035108     5.136504     
+    328000   14.310048           1000   0.68068243     5.152212     
+    329000   14.426048           1000   0.69123492     5.1679199    
+    330000   14.543349           1000   0.70326515     5.1836279    
+    331000   14.662021           1000   0.70551726     5.1993358    
+    332000   14.782194           1000   0.70514444     5.2150438    
+    333000   14.901573           1000   0.71102045     5.2307518    
+    334000   15.020642           1000   0.71336747     5.2464597    
+    335000   15.136739           1000   0.70816388     5.2621677    
+    336000   15.252554           1000   0.69502472     5.2778757    
+    337000   15.368496           1000   0.69314289     5.2935836    
+    338000   15.483744           1000   0.68565794     5.3092916    
+    339000   15.599584           1000   0.67268053     5.3249995    
+    340000   15.717342           1000   0.68313196     5.3407075    
+    341000   15.835594           1000   0.68782815     5.3564155    
+    342000   15.954546           1000   0.6989326      5.3721234    
+    343000   16.074184           1000   0.694926       5.3878314    
+    344000   16.193902           1000   0.7006474      5.4035394    
+    345000   16.314878           1000   0.70783177     5.4192473    
+    346000   16.434704           1000   0.71334276     5.4349553    
+    347000   16.554708           1000   0.72917419     5.4506633    
+    348000   16.673034           1000   0.74315705     5.4663712    
+    349000   16.791269           1000   0.76731311     5.4820792    
+    350000   16.912554           1000   0.79761434     5.4977871    
+    351000   17.03323            1000   0.80447724     5.5134951    
+    352000   17.155644           1000   0.80118728     5.5292031    
+    353000   17.281134           1000   0.77990459     5.544911     
+    354000   17.406672           1000   0.76453299     5.560619     
+    355000   17.532346           1000   0.76538392     5.576327     
+    356000   17.657256           1000   0.76310698     5.5920349    
+    357000   17.782477           1000   0.75897095     5.6077429    
+    358000   17.909642           1000   0.75071115     5.6234508    
+    359000   18.035032           1000   0.74034801     5.6391588    
+    360000   18.160696           1000   0.72671924     5.6548668    
+    361000   18.285089           1000   0.72111017     5.6705747    
+    362000   18.408849           1000   0.71875181     5.6862827    
+    363000   18.533901           1000   0.71469706     5.7019907    
+    364000   18.659326           1000   0.70470493     5.7176986    
+    365000   18.784109           1000   0.70863047     5.7334066    
+    366000   18.911344           1000   0.70850561     5.7491146    
+    367000   19.039756           1000   0.71413452     5.7648225    
+    368000   19.169907           1000   0.71314184     5.7805305    
+    369000   19.299066           1000   0.71309549     5.7962384    
+    370000   19.428116           1000   0.71132937     5.8119464    
+    371000   19.553027           1000   0.70788039     5.8276544    
+    372000   19.678121           1000   0.71780071     5.8433623    
+    373000   19.804465           1000   0.72352571     5.8590703    
+    374000   19.92949            1000   0.71723739     5.8747783    
+    375000   20.053554           1000   0.71556941     5.8904862    
+    376000   20.177991           1000   0.70935312     5.9061942    
+    377000   20.301972           1000   0.71551157     5.9219022    
+    378000   20.427612           1000   0.7235163      5.9376101    
+    379000   20.554742           1000   0.73896421     5.9533181    
+    380000   20.680899           1000   0.74906169     5.969026     
+    381000   20.805515           1000   0.75303336     5.984734     
+    382000   20.931483           1000   0.75359492     6.000442     
+    383000   21.05731            1000   0.75579354     6.0161499    
+    384000   21.184712           1000   0.75178368     6.0318579    
+    385000   21.310667           1000   0.74412159     6.0475659    
+    386000   21.433509           1000   0.7360955      6.0632738    
+    387000   21.554251           1000   0.73461103     6.0789818    
+    388000   21.674477           1000   0.72496617     6.0946897    
+    389000   21.794698           1000   0.7219047      6.1103977    
+    390000   21.914083           1000   0.71837013     6.1261057    
+    391000   22.033188           1000   0.71495923     6.1418136    
+    392000   22.152689           1000   0.71436707     6.1575216    
+    393000   22.271183           1000   0.71447834     6.1732296    
+    394000   22.389775           1000   0.71334298     6.1889375    
+    395000   22.509106           1000   0.71510229     6.2046455    
+    396000   22.628068           1000   0.7121714      6.2203535    
+    397000   22.746926           1000   0.70818894     6.2360614    
+    398000   22.865086           1000   0.70059455     6.2517694    
+    399000   22.982394           1000   0.69960089     6.2674773    
+    400000   23.100381           1000   0.70261998     6.2831853    
+Loop time of 23.1004 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 35345.963 tau/day, 8657.854 timesteps/s, 8.658 Matom-step/s
+92.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.263      | 2.1388     | 3.0295     |  58.6 |  9.26
+Neigh   | 0.012633   | 0.017793   | 0.023147   |   3.7 |  0.08
+Comm    | 7.8521     | 9.0474     | 10.284     |  39.6 | 39.17
+Output  | 0.0029549  | 0.004916   | 0.0068506  |   2.0 |  0.02
+Modify  | 8.3635     | 9.8066     | 11.142     |  41.0 | 42.45
+Other   |            | 2.085      |            |       |  9.03
+
+Nlocal:            250 ave         258 max         241 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Nghost:            412 ave         492 max         332 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:         1258.5 ave        1588 max         953 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 5034
+Ave neighs/atom = 5.034
+Neighbor list builds = 159
+Dangerous builds = 0
+Total wall time: 0:00:37

examples/granregion/log.27Nov18.granregion.box.g++.1

@@ -1,475 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-# pouring spheres into container box
-
-units		lj
-atom_style      sphere
-boundary        f f f
-dimension	3
-comm_modify     vel yes
-
-region          box block -10 10 -10 10 -10 10 units box
-create_box      2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff	* * gran/hooke
-
-region          container block -6 6 -6 6 -6 6 units box
-fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix             2 all nve/sphere
-fix		3 all gravity 1.0 vector 0 0 -1
-
-region          slab block -2 2 -2 2 -2 2 units box
-fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep	0.005
-
-compute         1 all temp
-compute_modify  1 dynamic/dof yes
-
-compute         2 all temp/sphere
-compute_modify  2 dynamic/dof yes
-
-thermo		100
-thermo_style	custom step atoms temp c_1 c_2 press
-thermo_modify   lost ignore
-compute_modify  thermo_temp dynamic/dof yes
-
-#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify	2 pad 5
-
-run	        5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.3
-  ghost atom cutoff = 1.3
-  binsize = 0.65, bins = 31 31 31
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke, perpetual
-      attributes: half, newton on, size
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.5855 | 0.5855 | 0.5855 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-       0        0            0            0            0            0 
-     100       21   0.54270729   0.54270729   0.26473526 0.0013567682 
-     200       21   0.87606961   0.87606961   0.42735103  0.002190174 
-     300       21    1.1428374    1.1428374   0.55748167 0.0028570936 
-     400       21    1.3543103    1.3543103   0.66829516 0.0033857758 
-     500       21    1.0677786    1.0677786   0.53582407 0.0045048164 
-     600       56    0.6744286    0.6744286    0.3502938 0.0047464584 
-     700       56   0.75569283   0.75569283   0.39779462 0.0051953882 
-     800       56   0.61597505   0.61597505   0.32943642 0.0086022783 
-     900       56   0.65260802   0.65260802   0.34474044 0.0059298996 
-    1000       56   0.51624952   0.51624952   0.28326898 0.0067827337 
-    1100       56   0.46050076   0.46050076   0.25656319 0.0061891094 
-    1200       81   0.39112346   0.39112346   0.21690172 0.0086559316 
-    1300       81   0.33302617   0.33302617   0.19109398 0.0033381104 
-    1400       81    0.3933533    0.3933533   0.21221692  0.004135078 
-    1500       81   0.35495297   0.35495297   0.19925984 0.0037374946 
-    1600       81   0.34150606   0.34150606   0.19025811 0.0053492835 
-    1700      100    0.2561647    0.2561647   0.14186278 0.0090767057 
-    1800      100   0.21124278   0.21124278   0.12154878 0.0028545759 
-    1900      100   0.21793955   0.21793955   0.12173867 0.0029049155 
-    2000      100   0.25530858   0.25530858   0.13892272 0.0035528009 
-    2100      100   0.24671808   0.24671808   0.13687783 0.0076812435 
-    2200      100   0.22465216   0.22465216   0.12513603 0.0042528715 
-    2300      100   0.19362854   0.19362854   0.10914305 0.0061173739 
-    2400      100  0.061627608  0.061627608  0.045907717 0.0010422721 
-    2500      100  0.052700901  0.052700901  0.038883014 0.0019341647 
-    2600      100  0.037332018  0.037332018  0.028357146 0.0028364476 
-    2700      100  0.033526602  0.033526602  0.024609055 0.00044524562 
-    2800      100    0.0194148    0.0194148  0.014491377 0.00056526591 
-    2900      100  0.012346108  0.012346108  0.009857017 0.00081855699 
-    3000      100    0.0107344    0.0107344  0.008669364 0.00040371396 
-    3100      100 0.0092678291 0.0092678291 0.0073003108 0.00033287397 
-    3200      100 0.0085847001 0.0085847001 0.0064045591 0.00023253547 
-    3300      100 0.0049475182 0.0049475182 0.0041173627 0.00019876269 
-    3400      100 0.0030471097 0.0030471097 0.0026940466 0.00013462604 
-    3500      100 0.0031188371 0.0031188371  0.002612223 0.00026148578 
-    3600      100 0.0017616584 0.0017616584 0.0017464137 0.00019049724 
-    3700      100 0.0015475923 0.0015475923 0.0015560356 0.00025062814 
-    3800      100 0.0012547887 0.0012547887 0.0012622678 0.00014132236 
-    3900      100 0.0010047282 0.0010047282 0.0010379262 9.7665594e-05 
-    4000      100 0.00080895307 0.00080895307 0.00088263027 8.1278842e-05 
-    4100      100 0.00079078739 0.00079078739 0.00085810727 8.1271694e-05 
-    4200      100 0.00075192318 0.00075192318 0.00083085046 8.9352453e-05 
-    4300      100 0.00063546457 0.00063546457 0.00073222177 8.9264255e-05 
-    4400      100 0.00062398391 0.00062398391 0.00071312118 8.4200615e-05 
-    4500      100 0.00056464934 0.00056464934 0.00066087801 9.2097641e-05 
-    4600      100 0.00066951894 0.00066951894 0.00071633313 8.2457941e-05 
-    4700      100  0.001128837  0.001128837 0.00095293877 0.00011716361 
-    4800      100 0.00049580391 0.00049580391 0.00056710488 0.00010718794 
-    4900      100 0.00054374371 0.00054374371 0.00058671699 5.6580257e-05 
-    5000      100 0.00043016232 0.00043016232 0.00050264172 2.8640786e-05 
-Loop time of 0.0807264 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 26757050.955 tau/day, 61937.618 timesteps/s
-97.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0089066  | 0.0089066  | 0.0089066  |   0.0 | 11.03
-Neigh   | 0.017107   | 0.017107   | 0.017107   |   0.0 | 21.19
-Comm    | 0.00091505 | 0.00091505 | 0.00091505 |   0.0 |  1.13
-Output  | 0.00051451 | 0.00051451 | 0.00051451 |   0.0 |  0.64
-Modify  | 0.047671   | 0.047671   | 0.047671   |   0.0 | 59.05
-Other   |            | 0.005612   |            |       |  6.95
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    158 ave 158 max 158 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 158
-Ave neighs/atom = 1.58
-Neighbor list builds = 310
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-5000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
-run	        5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-    5000      100 0.00043016232 0.00043016232 0.00050264172 2.8677624e-05 
-    5100      100   0.56489668   0.56489668   0.31137762  0.011848041 
-    5200      100   0.66068288   0.66068288   0.35915482  0.010199755 
-    5300      100   0.74068022   0.74068022   0.39643217  0.010806409 
-    5400      100   0.80913562   0.80913562   0.42748505   0.01190892 
-    5500      100   0.89409135   0.89409135   0.46135116  0.013093474 
-    5600      100   0.97585093   0.97585093   0.50021126  0.013588886 
-    5700      100    1.0151954    1.0151954    0.5174624   0.01601347 
-    5800      100    1.0452728    1.0452728   0.53122496   0.01879329 
-    5900      100    1.0881689    1.0881689   0.55152229  0.017120714 
-    6000      100    1.1133186    1.1133186    0.5638022  0.017284617 
-    6100      100    1.1532099    1.1532099   0.58310076  0.017031384 
-    6200      100    1.1798849    1.1798849    0.5959516  0.017971323 
-    6300      100      1.19387      1.19387   0.60173877  0.020140984 
-    6400      100    1.2126705    1.2126705   0.61086899  0.018426638 
-    6500      100    1.2137646    1.2137646   0.61284198  0.019127381 
-    6600      100    1.2339012    1.2339012   0.62199324  0.019378799 
-    6700      100    1.2439326    1.2439326   0.62488425  0.021049447 
-    6800      100    1.2489549    1.2489549    0.6278167  0.019552409 
-    6900      100    1.2733303    1.2733303   0.63898149  0.020237284 
-    7000      100    1.2835029    1.2835029    0.6440245  0.020798586 
-    7100      100    1.2866111    1.2866111   0.64522896  0.020355019 
-    7200      100    1.2886381    1.2886381    0.6467497   0.02062322 
-    7300      100    1.2885085    1.2885085   0.64617988  0.020350755 
-    7400      100    1.2912349    1.2912349   0.64691898  0.020197503 
-    7500      100    1.2963062    1.2963062   0.64926335  0.020349791 
-    7600      100    1.3016488    1.3016488   0.65150178  0.021001457 
-    7700      100    1.3009311    1.3009311   0.65106234  0.021546471 
-    7800      100    1.3016987    1.3016987   0.65143099  0.020994967 
-    7900      100    1.3028811    1.3028811   0.65164558  0.022200425 
-    8000      100    1.3087855    1.3087855   0.65439023  0.021310808 
-    8100      100    1.3102001    1.3102001   0.65514941  0.021177764 
-    8200      100    1.3133931    1.3133931   0.65681861  0.021591267 
-    8300      100    1.3148898    1.3148898   0.65775353  0.021335384 
-    8400      100    1.3160355    1.3160355   0.65845913  0.021238095 
-    8500      100    1.3171797    1.3171797   0.65934185  0.021172983 
-    8600      100    1.3176785    1.3176785   0.65964311  0.020747457 
-    8700      100    1.3180425    1.3180425   0.66019624  0.021275913 
-    8800      100    1.3287501    1.3287501   0.66444242  0.021832635 
-    8900      100    1.3249847    1.3249847    0.6625848  0.021337451 
-    9000      100     1.326216     1.326216   0.66297827  0.021470663 
-    9100      100    1.3261662    1.3261662   0.66303852  0.021423573 
-    9200      100    1.3312132    1.3312132    0.6653609  0.021385943 
-    9300      100    1.3300976    1.3300976   0.66504574  0.021489888 
-    9400      100    1.3377335    1.3377335   0.66820989  0.021565001 
-    9500      100    1.3421956    1.3421956   0.67027168  0.022402346 
-    9600      100    1.3464217    1.3464217   0.67228206  0.021991922 
-    9700      100    1.3470623    1.3470623   0.67258349  0.022035729 
-    9800      100    1.3446725    1.3446725   0.67135725  0.022295251 
-    9900      100     1.343146     1.343146   0.67066672  0.022049041 
-   10000      100    1.3435397    1.3435397   0.67093067  0.022451365 
-Loop time of 0.247549 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 8725560.044 tau/day, 20198.056 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.031783   | 0.031783   | 0.031783   |   0.0 | 12.84
-Neigh   | 0.038383   | 0.038383   | 0.038383   |   0.0 | 15.51
-Comm    | 0.0012343  | 0.0012343  | 0.0012343  |   0.0 |  0.50
-Output  | 0.00056028 | 0.00056028 | 0.00056028 |   0.0 |  0.23
-Modify  | 0.1687     | 0.1687     | 0.1687     |   0.0 | 68.15
-Other   |            | 0.00689    |            |       |  2.78
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    199 ave 199 max 199 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 199
-Ave neighs/atom = 1.99
-Neighbor list builds = 621
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   10000      100    1.3435397    1.3435397   0.67093067  0.022411116 
-   10100      100   0.31352763   0.31352763   0.18877908   0.01321582 
-   10200      100   0.13367611   0.13367611  0.090010637 0.0074171016 
-   10300      100  0.068195658  0.068195658  0.052632714 0.0019696287 
-   10400      100  0.053814936  0.053814936  0.043037586 0.0017121584 
-   10500      100   0.04032072   0.04032072  0.032944572 0.0011809154 
-   10600      100  0.029178161  0.029178161  0.023951873 0.0007804529 
-   10700      100  0.025978206  0.025978206  0.021045025 0.00099531465 
-   10800      100  0.023205036  0.023205036   0.01898502 0.00040036401 
-   10900      100  0.019994638  0.019994638  0.016451227 0.00027385559 
-   11000      100  0.017838131  0.017838131  0.014730762 0.00040399762 
-   11100      100  0.014863196  0.014863196  0.012314308 0.00019097464 
-   11200      100  0.012131256  0.012131256  0.010102122 0.00018514926 
-   11300      100  0.010881385  0.010881385 0.0090013541 0.00016579157 
-   11400      100 0.0076519814 0.0076519814 0.0064604568 0.00035399997 
-   11500      100 0.0067507315 0.0067507315 0.0057378868 0.00049116726 
-   11600      100 0.0053146649 0.0053146649 0.0047005938 0.00019625233 
-   11700      100 0.0044162463 0.0044162463 0.0039534657 0.00012548039 
-   11800      100 0.0037025387 0.0037025387 0.0033604103 6.2969827e-05 
-   11900      100 0.0032632211 0.0032632211 0.0030406641 8.1600622e-05 
-   12000      100 0.0028944057 0.0028944057 0.0026875858 6.6435833e-05 
-   12100      100 0.0027644728 0.0027644728 0.0025859762 5.5899271e-05 
-   12200      100  0.002480367  0.002480367 0.0023685117 6.0201418e-05 
-   12300      100 0.0024136475 0.0024136475 0.0023107986 4.4386874e-05 
-   12400      100 0.0021911567 0.0021911567 0.0021413262 5.0213175e-05 
-   12500      100 0.0019775905 0.0019775905 0.0019927698 0.00035250097 
-   12600      100 0.0017410363 0.0017410363  0.001830428 5.7885177e-05 
-   12700      100 0.0015749276 0.0015749276 0.0016816771 4.5530192e-05 
-   12800      100 0.0015187705 0.0015187705 0.0016218625 4.0589413e-05 
-   12900      100 0.0014778376 0.0014778376  0.001580232 4.0085455e-05 
-   13000      100 0.0014693491 0.0014693491 0.0015681809 4.0407656e-05 
-   13100      100 0.0014434495 0.0014434495 0.0015356278 5.7849212e-05 
-   13200      100 0.0014121959 0.0014121959 0.0015058758 3.2720737e-05 
-   13300      100 0.0012876041 0.0012876041 0.0013838998 3.7725702e-05 
-   13400      100 0.0012304951 0.0012304951 0.0013373457 3.6784546e-05 
-   13500      100 0.0011954303 0.0011954303 0.0012877627 3.6584963e-05 
-   13600      100 0.0011028947 0.0011028947 0.0011955404 2.3767582e-05 
-   13700      100 0.0010611762 0.0010611762 0.0011504675 3.485879e-05 
-   13800      100 0.0010080835 0.0010080835 0.0010997919 3.7905404e-05 
-   13900      100 0.00096495712 0.00096495712 0.0010530767 3.5273885e-05 
-   14000      100 0.00094945029 0.00094945029 0.0010409175 3.3718395e-05 
-   14100      100 0.00092386757 0.00092386757 0.0010217415 3.3313256e-05 
-   14200      100 0.00088928389 0.00088928389  0.000983023 3.290941e-05 
-   14300      100 0.00082696485 0.00082696485 0.00092690771 3.1651431e-05 
-   14400      100 0.00081086188 0.00081086188 0.00091681096 3.1845632e-05 
-   14500      100 0.00077732305 0.00077732305 0.00087592983 4.8087361e-05 
-   14600      100 0.00073386005 0.00073386005 0.00082546873 3.0892065e-05 
-   14700      100 0.00068701098 0.00068701098 0.00075953521 0.00010208859 
-   14800      100 0.00065860451 0.00065860451 0.00073738846 2.9272912e-05 
-   14900      100 0.00064706564 0.00064706564 0.00072748391 2.9817955e-05 
-   15000      100 0.00064227996 0.00064227996 0.00070964586 3.2547768e-05 
-Loop time of 0.0840213 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 25707757.817 tau/day, 59508.699 timesteps/s
-98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.01004    | 0.01004    | 0.01004    |   0.0 | 11.95
-Neigh   | 0.0057366  | 0.0057366  | 0.0057366  |   0.0 |  6.83
-Comm    | 0.00086808 | 0.00086808 | 0.00086808 |   0.0 |  1.03
-Output  | 0.00049472 | 0.00049472 | 0.00049472 |   0.0 |  0.59
-Modify  | 0.060893   | 0.060893   | 0.060893   |   0.0 | 72.47
-Other   |            | 0.005989   |            |       |  7.13
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    151 ave 151 max 151 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 151
-Ave neighs/atom = 1.51
-Neighbor list builds = 92
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-15000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
-run	        5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   15000      100 0.00064227996 0.00064227996 0.00070964586 3.2291286e-05 
-   15100      100   0.81230775   0.81230775   0.53266834  0.010948517 
-   15200      100   0.87957637   0.87957637   0.57559572  0.012401402 
-   15300      100    1.0262431    1.0262431   0.66535656  0.015239294 
-   15400      100    1.2863564    1.2863564   0.82026439  0.020115365 
-   15500      100    1.4721549    1.4721549   0.92138954  0.022400442 
-   15600      100    1.7140429    1.7140429    1.0103822   0.02558084 
-   15700      100    1.8963287    1.8963287    1.0916756  0.032032318 
-   15800      100    2.0741177    2.0741177    1.1706233  0.034251942 
-   15900      100    2.1434733    2.1434733    1.2054242  0.030132271 
-   16000      100    2.1409892    2.1409892    1.2019761  0.030914205 
-   16100      100    2.2496058    2.2496058    1.2476438  0.030939743 
-   16200      100     2.233356     2.233356    1.2499888  0.030097445 
-   16300      100    2.2673491    2.2673491     1.272321  0.030968524 
-   16400      100    2.3735648    2.3735648    1.3126117  0.034532377 
-   16500      100    2.4510087    2.4510087    1.3588349  0.036685351 
-   16600      100     2.497406     2.497406    1.3811443  0.032019982 
-   16700      100    2.6800518    2.6800518    1.4661941  0.037455527 
-   16800      100    2.8673997    2.8673997    1.5558303   0.03606532 
-   16900      100    3.1229488    3.1229488    1.6918439  0.039753213 
-   17000      100     3.117815     3.117815    1.6996841  0.046210837 
-   17100      100    3.3336225    3.3336225    1.7834517  0.047865361 
-   17200      100    3.1773164    3.1773164    1.7113961  0.047778334 
-   17300      100    3.4336759    3.4336759    1.8343073  0.049673718 
-   17400      100    3.3142326    3.3142326    1.7796613  0.055329946 
-   17500      100    3.3205493    3.3205493    1.7853946  0.043558145 
-   17600      100    3.2764553    3.2764553    1.7640702  0.051463316 
-   17700      100    3.1909643    3.1909643    1.7407995  0.043248948 
-   17800      100    3.1958324    3.1958324     1.735056  0.050123145 
-   17900      100    3.2431806    3.2431806    1.7380638  0.050838878 
-   18000      100    3.2967417    3.2967417    1.7705821  0.042176084 
-   18100      100    3.4270672    3.4270672    1.8459819  0.043589925 
-   18200      100    3.3638494    3.3638494    1.8159436  0.048949648 
-   18300      100    3.3192279    3.3192279    1.8122198  0.043629595 
-   18400      100    3.2627211    3.2627211     1.796316  0.045504529 
-   18500      100    3.5669172    3.5669172    1.9257062  0.048460393 
-   18600      100    3.5546411    3.5546411    1.9154318  0.046890968 
-   18700      100    3.7288485    3.7288485     2.011106  0.046906531 
-   18800      100    3.6800347    3.6800347    1.9936406  0.049985172 
-   18900      100    3.7151898    3.7151898     2.007659  0.050394561 
-   19000      100    3.9693368    3.9693368    2.1311549  0.053710204 
-   19100      100    3.6907732    3.6907732    1.9939387   0.05480136 
-   19200      100    3.8808777    3.8808777    2.0790125  0.055093552 
-   19300      100    3.8422142    3.8422142    2.0756951  0.058090774 
-   19400      100    3.7836875    3.7836875    2.0399805   0.06965907 
-   19500      100    4.0480195    4.0480195     2.169214  0.053420651 
-   19600      100     3.965917     3.965917    2.1245227  0.059077084 
-   19700      100    3.8980869    3.8980869    2.0956306  0.050857062 
-   19800      100     4.008079     4.008079    2.1501421  0.054938689 
-   19900      100    3.7244506    3.7244506    2.0080877  0.055481507 
-   20000      100    3.8146094    3.8146094    2.0541416  0.053187111 
-Loop time of 0.210396 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 10266363.999 tau/day, 23764.731 timesteps/s
-98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.013991   | 0.013991   | 0.013991   |   0.0 |  6.65
-Neigh   | 0.056947   | 0.056947   | 0.056947   |   0.0 | 27.07
-Comm    | 0.0013928  | 0.0013928  | 0.0013928  |   0.0 |  0.66
-Output  | 0.00054646 | 0.00054646 | 0.00054646 |   0.0 |  0.26
-Modify  | 0.13027    | 0.13027    | 0.13027    |   0.0 | 61.92
-Other   |            | 0.007249   |            |       |  3.45
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    144 ave 144 max 144 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 144
-Ave neighs/atom = 1.44
-Neighbor list builds = 910
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   20000      100    3.8146094    3.8146094    2.0541416  0.052956687 
-   20100      100    1.3848453    1.3848453   0.82244153  0.017544632 
-   20200      100   0.89469578   0.89469578   0.55929611    0.0111604 
-   20300      100   0.83962013   0.83962013   0.52665461  0.010396174 
-   20400      100   0.77264252   0.77264252   0.48961142 0.0095493901 
-   20500      100   0.78613208   0.78613208   0.48683715  0.012166835 
-   20600      100   0.88411633   0.88411633   0.52854942  0.011725323 
-   20700      100   0.89833225   0.89833225   0.52549693  0.012193413 
-   20800      100   0.90216089   0.90216089   0.51167019  0.014289685 
-   20900      100   0.98665057   0.98665057    0.5468893  0.013794318 
-   21000      100    0.7576342    0.7576342   0.42758791  0.011720156 
-   21100      100    0.3821563    0.3821563   0.23426423  0.005324458 
-   21200      100   0.17486973   0.17486973   0.12876582 0.0029726352 
-   21300      100   0.17940562   0.17940562   0.12400155 0.0026179917 
-   21400      100   0.15526876   0.15526876   0.10526802  0.002341177 
-   21500      100  0.079493361  0.079493361  0.062289324 0.0017379534 
-   21600      100  0.057299519  0.057299519  0.047939171 0.0020095941 
-   21700      100  0.056900097  0.056900097  0.045799124 0.0017782068 
-   21800      100  0.039847861  0.039847861  0.035138066 0.0018265057 
-   21900      100   0.03919167   0.03919167  0.031815619 0.0012160098 
-   22000      100  0.025499317  0.025499317  0.022126202 0.0010056809 
-   22100      100  0.018956113  0.018956113  0.017843095 0.0016109368 
-   22200      100  0.017337018  0.017337018  0.016063068 0.00042537508 
-   22300      100  0.014785686  0.014785686  0.013007571 0.00049466367 
-   22400      100  0.011754087  0.011754087  0.010399793 0.00042349151 
-   22500      100  0.010362474  0.010362474  0.009077435 0.00025198478 
-   22600      100 0.0089484896 0.0089484896 0.0079474121 0.00035239475 
-   22700      100 0.0089936432 0.0089936432 0.0077908763 0.00018548371 
-   22800      100 0.0068663718 0.0068663718 0.0064061667 0.00025641972 
-   22900      100 0.0050272392 0.0050272392 0.0046676214 0.00040466013 
-   23000      100 0.0049250142 0.0049250142 0.0044849467 0.00035704909 
-   23100      100 0.0050508148 0.0050508148 0.0043117775 0.00030051828 
-   23200      100 0.0037293467 0.0037293467 0.0033592517 0.00038108923 
-   23300      100 0.0032823722 0.0032823722 0.0030511575 0.00040421775 
-   23400      100 0.0026913866 0.0026913866 0.0025493429 9.2813733e-05 
-   23500      100 0.0025590632 0.0025590632 0.0024466447 8.4695125e-05 
-   23600      100 0.0025270441 0.0025270441 0.0024236554 8.4237376e-05 
-   23700      100 0.0026406527 0.0026406527 0.0024501963 0.00015009901 
-   23800      100 0.0024633391 0.0024633391 0.0023470594 3.8990761e-05 
-   23900      100 0.0029505606 0.0029505606 0.0025122613 4.9810757e-05 
-   24000      100 0.0019535519 0.0019535519 0.0019112421 3.5804751e-05 
-   24100      100 0.0017505151 0.0017505151  0.001726233 2.380737e-05 
-   24200      100 0.0015864857 0.0015864857 0.0015479949 1.963276e-05 
-   24300      100 0.0014535898 0.0014535898 0.0014221262 3.6607862e-05 
-   24400      100 0.0013744934 0.0013744934 0.0013523293 1.4522467e-05 
-   24500      100 0.0013286378 0.0013286378 0.0013097089 3.2389792e-05 
-   24600      100 0.0012093624 0.0012093624 0.0011617482 4.848694e-05 
-   24700      100 0.0011817062 0.0011817062 0.0011409092 3.8898899e-05 
-   24800      100 0.0011142524 0.0011142524 0.0010877723 1.4560662e-05 
-   24900      100 0.0010941199 0.0010941199 0.0010614415 7.0209336e-05 
-   25000      100 0.0010773559 0.0010773559 0.0010389783 1.3332279e-05 
-Loop time of 0.0912137 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 23680652.416 tau/day, 54816.325 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.010053   | 0.010053   | 0.010053   |   0.0 | 11.02
-Neigh   | 0.017597   | 0.017597   | 0.017597   |   0.0 | 19.29
-Comm    | 0.00092912 | 0.00092912 | 0.00092912 |   0.0 |  1.02
-Output  | 0.00049806 | 0.00049806 | 0.00049806 |   0.0 |  0.55
-Modify  | 0.056085   | 0.056085   | 0.056085   |   0.0 | 61.49
-Other   |            | 0.006052   |            |       |  6.63
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    143 ave 143 max 143 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 143
-Ave neighs/atom = 1.43
-Neighbor list builds = 289
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.27Nov18.granregion.box.g++.4

@@ -1,475 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-# pouring spheres into container box
-
-units		lj
-atom_style      sphere
-boundary        f f f
-dimension	3
-comm_modify     vel yes
-
-region          box block -10 10 -10 10 -10 10 units box
-create_box      2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
-  1 by 2 by 2 MPI processor grid
-
-pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff	* * gran/hooke
-
-region          container block -6 6 -6 6 -6 6 units box
-fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix             2 all nve/sphere
-fix		3 all gravity 1.0 vector 0 0 -1
-
-region          slab block -2 2 -2 2 -2 2 units box
-fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep	0.005
-
-compute         1 all temp
-compute_modify  1 dynamic/dof yes
-
-compute         2 all temp/sphere
-compute_modify  2 dynamic/dof yes
-
-thermo		100
-thermo_style	custom step atoms temp c_1 c_2 press
-thermo_modify   lost ignore
-compute_modify  thermo_temp dynamic/dof yes
-
-#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify	2 pad 5
-
-run	        5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.3
-  ghost atom cutoff = 1.3
-  binsize = 0.65, bins = 31 31 31
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke, perpetual
-      attributes: half, newton on, size
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.4834 | 0.4834 | 0.4834 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-       0        0            0            0            0            0 
-     100       21   0.54270729   0.54270729   0.26473526 0.0013567682 
-     200       21   0.87606961   0.87606961   0.42735103  0.002190174 
-     300       21    1.1428374    1.1428374   0.55748167 0.0028570936 
-     400       21    1.3543103    1.3543103   0.66829516 0.0033857758 
-     500       21    1.0677786    1.0677786   0.53582407 0.0045048164 
-     600       56    0.6744286    0.6744286    0.3502938 0.0047464584 
-     700       56   0.75569283   0.75569283   0.39779462 0.0051953882 
-     800       56   0.61597505   0.61597505   0.32943642 0.0086022783 
-     900       56   0.65260802   0.65260802   0.34474044 0.0059298996 
-    1000       56   0.51624952   0.51624952   0.28326898 0.0067827337 
-    1100       56   0.46050076   0.46050076   0.25656319 0.0061891094 
-    1200       81   0.39112346   0.39112346   0.21690172 0.0086559316 
-    1300       81   0.33302617   0.33302617   0.19109398 0.0033381104 
-    1400       81    0.3933533    0.3933533   0.21221692  0.004135078 
-    1500       81   0.35495297   0.35495297   0.19925984 0.0037374946 
-    1600       81   0.34150606   0.34150606   0.19025811 0.0053492835 
-    1700      100    0.2561647    0.2561647   0.14186278 0.0090767057 
-    1800      100   0.21124278   0.21124278   0.12154878  0.002854576 
-    1900      100   0.21793955   0.21793955   0.12173867 0.0029049175 
-    2000      100   0.25530858   0.25530858   0.13892272 0.0035528022 
-    2100      100   0.24671805   0.24671805   0.13687782 0.0076812357 
-    2200      100   0.22465212   0.22465212   0.12513612 0.0042526344 
-    2300      100   0.19362805   0.19362805   0.10914275 0.0061175383 
-    2400      100  0.061626039  0.061626039  0.045905953 0.0010393593 
-    2500      100  0.052690575  0.052690575  0.038879745 0.0018543933 
-    2600      100  0.037256691  0.037256691   0.02833916 0.0027683815 
-    2700      100  0.033416362  0.033416362  0.024551243 0.00046725913 
-    2800      100  0.019617758  0.019617758  0.014619416 0.00064550316 
-    2900      100  0.012313874  0.012313874 0.0098188153 0.00033470181 
-    3000      100  0.010948455  0.010948455 0.0087981878 0.00034401243 
-    3100      100  0.009359431  0.009359431 0.0073642412 0.00045497356 
-    3200      100  0.008129885  0.008129885 0.0061460516 0.00029944201 
-    3300      100 0.0050682533 0.0050682533 0.0042692811 0.00026543293 
-    3400      100 0.0031539312 0.0031539312 0.0027256511 0.00012475748 
-    3500      100 0.0023621311 0.0023621311 0.0021691817 0.0001186392 
-    3600      100 0.0018305354 0.0018305354 0.0018004128 0.00015926282 
-    3700      100 0.0016522492 0.0016522492 0.0017231072 0.0002193159 
-    3800      100 0.0011715102 0.0011715102 0.0012739973 0.0001747857 
-    3900      100 0.0010607606 0.0010607606 0.0010974725 0.00012476088 
-    4000      100 0.00087570802 0.00087570802 0.00095828935 6.5544103e-05 
-    4100      100 0.00078598203 0.00078598203 0.00088068743 9.4560761e-05 
-    4200      100 0.00088317454 0.00088317454 0.00092784605 8.1108122e-05 
-    4300      100 0.0015013254 0.0015013254 0.0012069505 8.8289686e-05 
-    4400      100 0.00070054041 0.00070054041 0.00079451193 5.195712e-05 
-    4500      100 0.00096259073 0.00096259073 0.00091232511 3.4895669e-05 
-    4600      100 0.00056641848 0.00056641848 0.00069083146 3.9657253e-05 
-    4700      100 0.0005455099 0.0005455099 0.00064816699 2.8131762e-05 
-    4800      100 0.00048254366 0.00048254366 0.00057192255 4.7914432e-05 
-    4900      100 0.00037108125 0.00037108125 0.00048035333 6.4711817e-05 
-    5000      100 0.00031290399 0.00031290399 0.00042398478 4.6025975e-05 
-Loop time of 0.075416 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 28641126.336 tau/day, 66298.904 timesteps/s
-93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0022948  | 0.0041364  | 0.0061705  |   2.8 |  5.48
-Neigh   | 0.0043123  | 0.0057145  | 0.0070784  |   1.8 |  7.58
-Comm    | 0.014259   | 0.018658   | 0.024313   |   3.3 | 24.74
-Output  | 0.0011525  | 0.001404   | 0.0015383  |   0.4 |  1.86
-Modify  | 0.0030508  | 0.014543   | 0.026602   |   9.5 | 19.28
-Other   |            | 0.03096    |            |       | 41.05
-
-Nlocal:    25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    5.5 ave 12 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:    39.75 ave 84 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 159
-Ave neighs/atom = 1.59
-Neighbor list builds = 310
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-5000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
-run	        5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-    5000      100 0.00031290399 0.00031290399 0.00042398478 4.4282259e-05 
-    5100      100   0.62661084   0.62661084   0.33840611  0.012020153 
-    5200      100   0.67371678   0.67371678   0.36218522 0.0093514044 
-    5300      100   0.75892331   0.75892331    0.4000747  0.010693252 
-    5400      100   0.86207426   0.86207426   0.44630388  0.013540097 
-    5500      100   0.96205334   0.96205334   0.49432848  0.017375079 
-    5600      100    1.0261194    1.0261194   0.52203912  0.016045333 
-    5700      100    1.0584366    1.0584366   0.53794336  0.018621676 
-    5800      100    1.0881674    1.0881674   0.55300469   0.01930602 
-    5900      100    1.1214233    1.1214233   0.56613492  0.021141141 
-    6000      100    1.1666836    1.1666836   0.58759377  0.017655361 
-    6100      100    1.1785775    1.1785775   0.59365148   0.01829443 
-    6200      100    1.2092305    1.2092305   0.60798809  0.018752443 
-    6300      100    1.2331787    1.2331787   0.62003386  0.020291021 
-    6400      100    1.2561616    1.2561616   0.63143643  0.019899235 
-    6500      100     1.284432     1.284432    0.6460504   0.02083284 
-    6600      100    1.2678801    1.2678801   0.63882384  0.019456553 
-    6700      100    1.2662641    1.2662641   0.63676836  0.020235578 
-    6800      100    1.2785484    1.2785484   0.64129093  0.020335162 
-    6900      100    1.2916608    1.2916608   0.64764298  0.020154225 
-    7000      100    1.2907774    1.2907774   0.64724849  0.020550885 
-    7100      100    1.3074473    1.3074473   0.65460147  0.020847362 
-    7200      100    1.3124592    1.3124592   0.65641332  0.020897348 
-    7300      100    1.3206191    1.3206191   0.66011491  0.021444077 
-    7400      100    1.3273988    1.3273988   0.66350669   0.02129418 
-    7500      100    1.3343911    1.3343911   0.66707269  0.021337376 
-    7600      100    1.3368998    1.3368998   0.66869327  0.021415901 
-    7700      100     1.330658     1.330658   0.66535295  0.021500761 
-    7800      100     1.330801     1.330801   0.66555123  0.022806058 
-    7900      100    1.3392828    1.3392828   0.66926796   0.02194009 
-    8000      100    1.3432728    1.3432728   0.67142337  0.022393719 
-    8100      100    1.3411612    1.3411612   0.66989302  0.022366895 
-    8200      100    1.3427451    1.3427451   0.67054285  0.021966329 
-    8300      100    1.3418147    1.3418147   0.67023132  0.022513459 
-    8400      100     1.346493     1.346493   0.67247837  0.022705366 
-    8500      100    1.3513958    1.3513958    0.6749092  0.022834077 
-    8600      100    1.3520297    1.3520297   0.67506261  0.023227676 
-    8700      100    1.3517157    1.3517157   0.67485073  0.023043414 
-    8800      100    1.3530071    1.3530071   0.67547212  0.022933766 
-    8900      100    1.3550454    1.3550454   0.67657277  0.022744182 
-    9000      100    1.3554069    1.3554069   0.67673505  0.022802134 
-    9100      100    1.3556675    1.3556675   0.67698335  0.022868449 
-    9200      100    1.3534709    1.3534709   0.67600677  0.022537792 
-    9300      100    1.3525103    1.3525103   0.67569499  0.022687849 
-    9400      100    1.3612673    1.3612673   0.67967213  0.022703588 
-    9500      100    1.3649439    1.3649439   0.68147385  0.023498539 
-    9600      100    1.3629376    1.3629376   0.68063814  0.023515579 
-    9700      100    1.3648924    1.3648924   0.68137104  0.023641856 
-    9800      100    1.3662063    1.3662063   0.68196538  0.023576884 
-    9900      100    1.3689695    1.3689695   0.68326751  0.023572622 
-   10000      100    1.3701139    1.3701139   0.68383343  0.023720885 
-Loop time of 0.174251 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 12395939.906 tau/day, 28694.305 timesteps/s
-96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0024631  | 0.010709   | 0.020461   |   8.0 |  6.15
-Neigh   | 0.0078361  | 0.012368   | 0.016955   |   4.0 |  7.10
-Comm    | 0.0059071  | 0.013641   | 0.023547   |   6.6 |  7.83
-Output  | 0.0011749  | 0.0021775  | 0.0030091  |   1.4 |  1.25
-Modify  | 0.015055   | 0.055709   | 0.097013   |  17.2 | 31.97
-Other   |            | 0.07965    |            |       | 45.71
-
-Nlocal:    25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    4.5 ave 10 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:    49.25 ave 101 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 197
-Ave neighs/atom = 1.97
-Neighbor list builds = 627
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   10000      100    1.3701139    1.3701139   0.68383343  0.023895921 
-   10100      100   0.25960098   0.25960098   0.15183967 0.0049554084 
-   10200      100   0.15017576   0.15017576   0.10081112 0.0045433238 
-   10300      100   0.10129671   0.10129671  0.078049099 0.0014012658 
-   10400      100   0.06742425   0.06742425  0.055603816 0.0010184792 
-   10500      100  0.053446366  0.053446366  0.045338293 0.00089291689 
-   10600      100  0.041898231  0.041898231  0.036081995 0.00060703885 
-   10700      100   0.03580041   0.03580041  0.031118724 0.00067731964 
-   10800      100  0.030933755  0.030933755  0.026372348 0.00039362325 
-   10900      100  0.027278004  0.027278004  0.022868898 0.0003680788 
-   11000      100  0.021566952  0.021566952  0.017994879 0.0013056062 
-   11100      100  0.019143625  0.019143625  0.015833865 0.00050998112 
-   11200      100  0.015659868  0.015659868  0.013119379 0.00012755696 
-   11300      100  0.013554605  0.013554605   0.01147808 0.00027393437 
-   11400      100   0.01204033   0.01204033  0.010273026 0.00033430792 
-   11500      100  0.010958991  0.010958991 0.0093924566 0.00049023273 
-   11600      100   0.01012553   0.01012553 0.0084556996 0.00021457333 
-   11700      100 0.0083584131 0.0083584131 0.0071118766 7.7149089e-05 
-   11800      100  0.007044883  0.007044883 0.0058675523 0.00036165381 
-   11900      100 0.0059875106 0.0059875106 0.0050610372 7.4095443e-05 
-   12000      100 0.0045180275 0.0045180275 0.0039006565 0.00014607704 
-   12100      100 0.0036631356 0.0036631356 0.0031154279 7.031064e-05 
-   12200      100 0.0034443424 0.0034443424 0.0029190637 0.00020974475 
-   12300      100 0.0030853504 0.0030853504 0.0026315266 3.4873541e-05 
-   12400      100 0.0025451749 0.0025451749 0.0022290833 0.00041551536 
-   12500      100 0.0021624857 0.0021624857 0.0019127734 2.6760761e-05 
-   12600      100 0.0020637862 0.0020637862 0.0018186641 4.9446655e-05 
-   12700      100 0.0019889538 0.0019889538 0.0017604689 3.326943e-05 
-   12800      100 0.0018706349 0.0018706349 0.0016669237 2.3327318e-05 
-   12900      100 0.0017472824 0.0017472824  0.001579469 8.816765e-05 
-   13000      100 0.0016034824 0.0016034824 0.0014549852 3.5407524e-05 
-   13100      100   0.00151798   0.00151798 0.0013826659 1.8754149e-05 
-   13200      100 0.0013049781 0.0013049781 0.0012137907 0.00015263775 
-   13300      100 0.0012270536 0.0012270536 0.0011590841  4.77636e-06 
-   13400      100 0.0011395128 0.0011395128 0.0010860297 2.5606328e-05 
-   13500      100 0.0010858414 0.0010858414 0.0010486713 5.8563931e-05 
-   13600      100 0.0010474389 0.0010474389  0.001015904 1.4319658e-05 
-   13700      100 0.00099241549 0.00099241549 0.00097825038 1.2281142e-05 
-   13800      100 0.00084449252 0.00084449252 0.00084141963 1.0451215e-05 
-   13900      100 0.00084004792 0.00084004792 0.00083755495 3.7174162e-05 
-   14000      100 0.00082183505 0.00082183505 0.00082027058 1.0170209e-05 
-   14100      100 0.00082377076 0.00082377076 0.00080489795 1.181976e-05 
-   14200      100 0.00076903208 0.00076903208 0.00076216608 4.4590341e-05 
-   14300      100 0.00075173269 0.00075173269 0.00074828209 2.2134371e-05 
-   14400      100 0.00074379148 0.00074379148 0.00074072001 1.5746014e-05 
-   14500      100 0.00072454029 0.00072454029 0.0007174429 8.9830398e-06 
-   14600      100 0.00072372648 0.00072372648 0.00071678769 9.1111512e-06 
-   14700      100 0.00071541587 0.00071541587 0.00070893868 7.8446375e-05 
-   14800      100 0.0006820307 0.0006820307 0.00066675502 8.4401299e-06 
-   14900      100 0.00067050627 0.00067050627 0.00065751846 0.0001228548 
-   15000      100 0.00064977132 0.00064977132 0.00062305247 7.8887775e-06 
-Loop time of 0.0746691 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 28927619.905 tau/day, 66962.083 timesteps/s
-96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0021737  | 0.0042608  | 0.0063519  |   3.2 |  5.71
-Neigh   | 0.0012126  | 0.0019009  | 0.0026193  |   1.6 |  2.55
-Comm    | 0.0023425  | 0.0092477  | 0.016876   |   7.2 | 12.38
-Output  | 0.0010619  | 0.0017995  | 0.0030522  |   1.8 |  2.41
-Modify  | 0.00097013 | 0.017151   | 0.03415    |  12.3 | 22.97
-Other   |            | 0.04031    |            |       | 53.98
-
-Nlocal:    25 ave 55 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    3.75 ave 9 max 0 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs:    42.5 ave 88 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 170
-Ave neighs/atom = 1.7
-Neighbor list builds = 97
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-15000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
-run	        5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   15000      100 0.00064977132 0.00064977132 0.00062305247 7.9405607e-06 
-   15100      100    1.0123899    1.0123899   0.66185504  0.014587215 
-   15200      100    1.0332828    1.0332828   0.67443308  0.014002815 
-   15300      100    1.0804076    1.0804076   0.72450056  0.016985272 
-   15400      100    1.2868163    1.2868163    0.8708132  0.022190597 
-   15500      100    1.5180471    1.5180471   0.99613124  0.026761866 
-   15600      100    1.5422016    1.5422016    1.0021746  0.024490139 
-   15700      100    1.7142241    1.7142241    1.0611146    0.0301368 
-   15800      100    1.8747057    1.8747057    1.1207858  0.027612699 
-   15900      100    1.9294819    1.9294819    1.1289025  0.027270228 
-   16000      100     1.953275     1.953275    1.1264475  0.031568811 
-   16100      100    2.0434228    2.0434228    1.1665365  0.026358952 
-   16200      100    2.2129393    2.2129393    1.2448327  0.029613382 
-   16300      100    2.2558224    2.2558224    1.2373264  0.028306021 
-   16400      100     2.367398     2.367398     1.293448  0.029659303 
-   16500      100    2.4221549    2.4221549    1.3198966  0.032541712 
-   16600      100     2.510283     2.510283    1.3618001  0.034740544 
-   16700      100    2.6776293    2.6776293    1.4508262  0.034556341 
-   16800      100    2.8095841    2.8095841    1.5190571  0.035183782 
-   16900      100    2.8485646    2.8485646    1.5344387  0.037153336 
-   17000      100    3.0298285    3.0298285    1.6321623  0.040745906 
-   17100      100    3.0218054    3.0218054    1.6187189  0.042082135 
-   17200      100    3.1981705    3.1981705    1.7090597  0.041770208 
-   17300      100    3.3178559    3.3178559    1.7723201  0.044604756 
-   17400      100    3.3940903    3.3940903    1.8229846  0.049231759 
-   17500      100    3.3274817    3.3274817    1.7870996  0.051649102 
-   17600      100    3.3204358    3.3204358     1.791527  0.043875639 
-   17700      100    3.2185649    3.2185649    1.7480866  0.049941218 
-   17800      100    3.2507826    3.2507826    1.7727758  0.048622479 
-   17900      100    3.2432767    3.2432767    1.7796296  0.044343902 
-   18000      100    3.0841272    3.0841272    1.6978832  0.045344433 
-   18100      100    3.0953909    3.0953909     1.699898  0.040070963 
-   18200      100    3.1405704    3.1405704    1.7316463  0.042528194 
-   18300      100    3.1904871    3.1904871    1.7555188  0.041141165 
-   18400      100    3.3256779    3.3256779    1.8243767  0.043908318 
-   18500      100    3.5161823    3.5161823    1.9150861  0.045165166 
-   18600      100    3.5668273    3.5668273    1.9217975  0.048127705 
-   18700      100    3.6648305    3.6648305    1.9685241  0.051205352 
-   18800      100    3.9000502    3.9000502    2.0886668   0.05262835 
-   18900      100    4.0217758    4.0217758    2.1465498  0.054502839 
-   19000      100    3.8431174    3.8431174    2.0581611  0.054852333 
-   19100      100    4.1721454    4.1721454    2.2221193  0.053831555 
-   19200      100    3.9061181    3.9061181     2.096323  0.058077678 
-   19300      100    4.0191085    4.0191085    2.1408069   0.05475437 
-   19400      100    3.8840871    3.8840871    2.0887677  0.061905092 
-   19500      100    3.8388062    3.8388062    2.0567095  0.051076414 
-   19600      100    3.6331742    3.6331742    1.9574769   0.04748008 
-   19700      100    3.6996954    3.6996954    1.9887285  0.053305043 
-   19800      100    3.8649872    3.8649872    2.0827424  0.060484008 
-   19900      100    3.8305733    3.8305733    2.0700281  0.052926584 
-   20000      100    3.7948463    3.7948463    2.0657301  0.048516953 
-Loop time of 0.156359 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 13814330.011 tau/day, 31977.616 timesteps/s
-94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0040646  | 0.0058124  | 0.0074518  |   1.6 |  3.72
-Neigh   | 0.014813   | 0.018389   | 0.020829   |   1.6 | 11.76
-Comm    | 0.031892   | 0.034103   | 0.036658   |   1.0 | 21.81
-Output  | 0.0013497  | 0.0019822  | 0.003484   |   2.0 |  1.27
-Modify  | 0.031006   | 0.046878   | 0.056364   |   4.5 | 29.98
-Other   |            | 0.0492     |            |       | 31.46
-
-Nlocal:    25 ave 37 max 10 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    3.75 ave 6 max 2 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-Neighs:    36.25 ave 57 max 9 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-
-Total # of neighbors = 145
-Ave neighs/atom = 1.45
-Neighbor list builds = 921
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.734 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   20000      100    3.7948463    3.7948463    2.0657301  0.048381317 
-   20100      100    1.1359931    1.1359931   0.70170151  0.015300556 
-   20200      100   0.87354617   0.87354617   0.55969299  0.012181983 
-   20300      100   0.84424484   0.84424484   0.52849351  0.017724782 
-   20400      100   0.82422562   0.82422562   0.50175766 0.0098154181 
-   20500      100   0.83731289   0.83731289   0.49814627  0.010465327 
-   20600      100   0.93125924   0.93125924   0.53803834  0.011624902 
-   20700      100    1.0810919    1.0810919   0.60974741   0.01425935 
-   20800      100    1.0646343    1.0646343   0.60037545  0.013418132 
-   20900      100    1.0608055    1.0608055   0.58353908  0.015119612 
-   21000      100   0.68173094   0.68173094    0.3941588 0.0099947535 
-   21100      100   0.35407592   0.35407592   0.21306735 0.0043859494 
-   21200      100   0.19247432   0.19247432   0.12989264 0.0031808422 
-   21300      100   0.13493768   0.13493768  0.093987634 0.0025990872 
-   21400      100  0.085735857  0.085735857  0.062091707  0.001434207 
-   21500      100  0.074307566  0.074307566   0.05224051 0.0022163094 
-   21600      100  0.069932382  0.069932382  0.045388838 0.0020296572 
-   21700      100  0.041749712  0.041749712  0.031422931  0.001211155 
-   21800      100   0.03378055   0.03378055  0.026248846 0.0020596463 
-   21900      100  0.030608528  0.030608528  0.022868294 0.0016282878 
-   22000      100  0.025632448  0.025632448  0.019606402 0.0011659657 
-   22100      100  0.013785062  0.013785062  0.011561769 0.00069006322 
-   22200      100  0.013139066  0.013139066  0.010559726 0.00038424576 
-   22300      100   0.01455318   0.01455318  0.011094558 0.00054735929 
-   22400      100 0.0096885414 0.0096885414  0.008012617 0.00055875777 
-   22500      100 0.0081193116 0.0081193116  0.006802973 0.00052914932 
-   22600      100 0.0057159621 0.0057159621 0.0048680253 0.00054864875 
-   22700      100 0.0052344376 0.0052344376 0.0045511708 0.00026333033 
-   22800      100 0.0054554177 0.0054554177 0.0045005479 0.0002085972 
-   22900      100 0.0039455776 0.0039455776 0.0035287888 0.00022514017 
-   23000      100 0.0042620461 0.0042620461 0.0035747729 0.00020030999 
-   23100      100 0.0035303095 0.0035303095 0.0031995108 0.00016007298 
-   23200      100 0.0029747457 0.0029747457 0.0027095904 0.00029775807 
-   23300      100 0.0032404433 0.0032404433  0.002769389 0.00019627995 
-   23400      100 0.0024965262 0.0024965262 0.0022343473 0.00018870133 
-   23500      100   0.00251617   0.00251617 0.0022533604 0.0002661237 
-   23600      100 0.0025923653 0.0025923653 0.0022887204 0.00018475201 
-   23700      100 0.0023016545 0.0023016545 0.0019829032 0.00014888334 
-   23800      100 0.0028358441 0.0028358441 0.0021790504 0.00064613131 
-   23900      100 0.0016682403 0.0016682403 0.0014930521 8.8407075e-05 
-   24000      100 0.0016341577 0.0016341577 0.0014597606 0.00011262081 
-   24100      100 0.0015433636 0.0015433636 0.0013981581 8.364568e-05 
-   24200      100 0.0015033978 0.0015033978 0.0013582013 8.4539006e-05 
-   24300      100 0.0014513098 0.0014513098 0.0012943981 0.00010546194 
-   24400      100 0.0013293352 0.0013293352  0.001206366 8.4967509e-05 
-   24500      100 0.0013732518 0.0013732518  0.001202532 0.00014787559 
-   24600      100 0.00091890041 0.00091890041 0.00084499923 0.00010080638 
-   24700      100 0.00083467915 0.00083467915 0.00077071316 5.3934025e-05 
-   24800      100 0.00080701934 0.00080701934 0.0007477161 5.3982095e-05 
-   24900      100 0.00080620771 0.00080620771 0.0007471026 5.3581294e-05 
-   25000      100 0.00080568604 0.00080568604 0.00074625735 5.3574637e-05 
-Loop time of 0.0792506 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 27255302.560 tau/day, 63090.978 timesteps/s
-95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0023611  | 0.0047854  | 0.0077851  |   3.4 |  6.04
-Neigh   | 0.0042653  | 0.005571   | 0.0067258  |   1.5 |  7.03
-Comm    | 0.0077977  | 0.013373   | 0.019515   |   4.4 | 16.87
-Output  | 0.0010924  | 0.0017727  | 0.0030222  |   1.8 |  2.24
-Modify  | 0.0023608  | 0.015964   | 0.030545   |  10.5 | 20.14
-Other   |            | 0.03778    |            |       | 47.68
-
-Nlocal:    25 ave 50 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    5 ave 10 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    35.75 ave 78 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 143
-Ave neighs/atom = 1.43
-Neighbor list builds = 287
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.27Nov18.granregion.funnel.g++.1

@@ -1,601 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable	name string funnel_pour
-
-thermo_modify	flush yes
-units 		si
-variable	PI equal 3.141592653589
-variable	seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	xlo equal 10
-variable	xhi equal 40
-variable	ylo equal 10
-variable	yhi equal 40
-variable	zlo equal -20
-variable	zhi equal 50
-
-variable	xc equal 25
-variable	yc equal 25
-
-variable	zconehi equal 50
-variable	zconelo equal 10
-variable	zcyllo equal 0
-variable	radconelo equal 2
-variable	radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable 	skin equal ${rhi}
-variable 	skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	density equal 1.0
-variable	EYoung equal 10^5
-variable 	Poisson equal 2.0/7.0
-variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+0.285714285714286))
-
-variable	gravity equal 1.0
-
-variable	reff equal 0.5*(${rhi}+${rlo})
-variable	reff equal 0.5*(0.5+${rlo})
-variable	reff equal 0.5*(0.5+0.25)
-variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable        kt equal 4.0*${GShear}/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable	a equal (-2.0*log(${coeffRes})/${PI})^2
-variable	a equal (-2.0*log(0.1)/${PI})^2
-variable	a equal (-2.0*log(0.1)/3.141592653589)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 903.503751814138*0.5
-
-variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable	dt equal ${tcol}*0.05
-variable	dt equal 0.00210943016014969*0.05
-timestep	${dt}
-timestep	0.000105471508007485
-
-###############################################
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		off
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 -20 ${zhi}
-region		boxreg block 10 40 10 40 -20 50
-create_box	1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} bin
-neighbor        0.5 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0
-  ghost atom cutoff = 0
-  binsize = 30, bins = 1 1 3
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
-
-region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
-region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
-
-region		hopreg union 2 conereg cylreg
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-
-fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes
-Step CPU Atoms KinEng 
-       0            0        0           -0 
-    1000   0.63593698     2000           -0 
-    2000    1.0282419     2000           -0 
-    3000    1.4184453     2000           -0 
-    4000    1.8055785     2000           -0 
-    5000    2.1941335     2000           -0 
-    6000    2.5804653     2000           -0 
-    7000    2.9660621     2000           -0 
-    8000    3.3506265     2000           -0 
-    9000    3.7344413     2000           -0 
-   10000    4.1212304     2000           -0 
-   11000    4.5044594     2000           -0 
-   12000    4.8875456     2000           -0 
-   13000    5.2698007     2000           -0 
-   14000    5.6527214     2000           -0 
-   15000    6.0349295     2000           -0 
-   16000    6.4172938     2000           -0 
-   17000    6.8001184     2000           -0 
-   18000    7.1826644     2000           -0 
-   19000    7.5654378     2000           -0 
-   20000    7.9511659     2000           -0 
-Loop time of 7.95118 on 1 procs for 20000 steps with 2000 atoms
-
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.6189     | 0.6189     | 0.6189     |   0.0 |  7.78
-Neigh   | 0.09361    | 0.09361    | 0.09361    |   0.0 |  1.18
-Comm    | 0.016098   | 0.016098   | 0.016098   |   0.0 |  0.20
-Output  | 0.00048828 | 0.00048828 | 0.00048828 |   0.0 |  0.01
-Modify  | 6.9973     | 6.9973     | 6.9973     |   0.0 | 88.00
-Other   |            | 0.2248     |            |       |  2.83
-
-Nlocal:    2000 ave 2000 max 2000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1537 ave 1537 max 1537 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1537
-Ave neighs/atom = 0.7685
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Per MPI rank memory allocation (min/avg/max) = 12.77 | 12.77 | 12.77 Mbytes
-Step CPU Atoms KinEng 
-   20000            0     2000    6443.7665 
-   21000    0.3826313     2000    6572.3531 
-   22000   0.76688981     2000    6723.8376 
-   23000    1.1534231     2000    6853.1812 
-   24000    1.5391715     2000    6976.0209 
-   25000    1.9263508     2000    7096.9955 
-   26000    2.3168406     2000    7215.5795 
-   27000    2.7065961     2000    7349.2382 
-   28000     3.096664     2000    7471.8719 
-   29000    3.4905531     2000    7574.8228 
-   30000    3.8877606     2000    7659.3836 
-   31000    4.2839894     2000    7703.6856 
-   32000    4.6859732     2000     7644.279 
-   33000    5.0932801     2000    7526.6944 
-   34000    5.5045564     2000    7370.0821 
-   35000    5.9206297     2000    7193.0457 
-   36000     6.343729     2000    6990.9899 
-   37000    6.7719142     2000    6849.2841 
-   38000    7.2016783     2000    6701.7433 
-   39000    7.6354482     2000    6538.9557 
-   40000     8.078445     2000    6381.9346 
-   41000    8.5191586     2000    6217.5253 
-   42000    8.9630713     2000    6093.5344 
-   43000    9.4097741     2000    5943.0479 
-   44000    9.8652256     2000    5841.0782 
-   45000    10.331057     2000    5652.8319 
-   46000    10.803253     2000    5476.1466 
-   47000    11.278766     2000    5267.7855 
-   48000    11.759121     2000    5131.4036 
-   49000    12.248896     2000    4972.7696 
-   50000    12.747719     2000    4867.0868 
-   51000    13.246704     2000     4681.897 
-   52000    13.757842     2000    4506.8185 
-   53000    14.276078     2000    4346.8045 
-   54000    14.795933     2000    4193.8194 
-   55000    15.311241     2000    4058.2049 
-   56000    15.828737     2000    3879.0325 
-   57000    16.359453     2000    3696.3154 
-   58000    16.905406     2000    3504.0399 
-   59000    17.460454     2000    3284.6522 
-   60000    18.027276     2000    3061.0727 
-   61000    18.586931     2000    2874.2926 
-   62000    19.158563     2000    2653.0722 
-   63000    19.738442     2000    2437.4941 
-   64000    20.331411     2000    2124.1876 
-   65000    20.936204     2000    1864.5661 
-   66000    21.547443     2000    1610.2335 
-   67000    22.166888     2000    1390.0428 
-   68000    22.789106     2000    1163.7679 
-   69000    23.416016     2000     933.0928 
-   70000    24.038879     2000    745.66667 
-   71000    24.663115     2000    605.58458 
-   72000    25.294193     2000    444.31183 
-   73000    25.932019     2000    357.19162 
-   74000    26.568184     2000    291.16762 
-   75000    27.203393     2000    230.58362 
-   76000    27.836079     2000    197.59502 
-   77000    28.467344     2000    166.55702 
-   78000    29.099997     2000    139.89052 
-   79000    29.741694     2000     117.1145 
-   80000    30.388097     2000    100.12353 
-   81000    31.036193     2000    85.233155 
-   82000    31.688463     2000    71.145302 
-   83000    32.343411     2000    61.545348 
-   84000    32.999346     2000    54.099358 
-   85000    33.652976     2000    46.922028 
-   86000    34.306931     2000    41.606645 
-   87000    34.967787     2000    37.462793 
-   88000    35.633721     2000    33.698298 
-   89000    36.310035     2000    29.340455 
-   90000    36.995441     2000    26.072122 
-   91000     37.67904     2000     23.20848 
-   92000    38.367699     2000    21.015862 
-   93000    39.058641     2000    20.134175 
-   94000    39.749342     2000    19.196075 
-   95000    40.442651     2000    18.285127 
-   96000    41.140177     2000    17.476411 
-   97000    41.840761     2000     16.55882 
-   98000    42.543845     2000    15.444541 
-   99000    43.256415     2000     14.41642 
-  100000     43.97382     2000    13.818738 
-  101000    44.684596     2000    12.878373 
-  102000    45.401082     2000     12.11804 
-  103000    46.120936     2000    11.016885 
-  104000     46.83935     2000    10.531044 
-  105000    47.559419     2000     10.46735 
-  106000    48.286016     2000    10.246007 
-  107000    49.012266     2000    9.6423041 
-  108000     49.74013     2000    9.3948808 
-  109000    50.471961     2000    9.5178141 
-  110000    51.206152     2000    9.4143884 
-  111000    51.939123     2000    9.5058226 
-  112000    52.673443     2000    9.6911516 
-  113000    53.410485     2000    9.7756849 
-  114000    54.152537     2000    9.3876232 
-  115000    54.891784     2000    8.6725333 
-  116000    55.631474     2000    8.6691065 
-  117000    56.371762     2000    8.0156055 
-  118000    57.110131     2000    7.9150786 
-  119000      57.8533     2000    7.5310892 
-  120000    58.599064     2000    7.2940498 
-  121000    59.340753     2000    6.8347898 
-  122000    60.084676     2000     6.696484 
-  123000    60.826952     2000    6.7799146 
-  124000    61.569413     2000    6.7901567 
-  125000    62.316334     2000    6.7532108 
-  126000    63.061374     2000     6.762162 
-  127000    63.806385     2000    6.6317366 
-  128000    64.555969     2000    6.8246399 
-  129000    65.308131     2000    6.9130358 
-  130000    66.060967     2000    7.1750566 
-  131000    66.809725     2000    6.9507379 
-  132000    67.559796     2000    6.7987445 
-  133000    68.314249     2000    6.8535775 
-  134000    69.065513     2000    7.0255144 
-  135000    69.817604     2000    6.7381064 
-  136000    70.572079     2000    6.5567748 
-  137000    71.324444     2000    6.2655395 
-  138000    72.079147     2000    6.1923013 
-  139000    72.831323     2000    6.0958081 
-  140000     73.59117     2000    5.9185709 
-  141000    74.343753     2000    5.9151241 
-  142000    75.096509     2000    5.4743035 
-  143000    75.852151     2000     5.438642 
-  144000    76.605005     2000    4.6646664 
-  145000    77.357571     2000    4.6899837 
-  146000    78.113125     2000    4.5357917 
-  147000    78.867751     2000    4.5993842 
-  148000    79.625344     2000    4.7076884 
-  149000     80.37992     2000    4.8306642 
-  150000    81.143175     2000    4.8282147 
-  151000    81.899326     2000     4.546308 
-  152000    82.658645     2000    4.6700755 
-  153000     83.41837     2000    4.7557633 
-  154000     84.17509     2000    4.9004538 
-  155000    84.934161     2000    5.0552949 
-  156000    85.695466     2000    4.0672495 
-  157000    86.453115     2000    3.5819543 
-  158000    87.212663     2000    3.3533477 
-  159000    87.967768     2000    3.3281001 
-  160000    88.729631     2000    3.0831743 
-  161000    89.498983     2000    3.0519269 
-  162000    90.259424     2000    3.0951675 
-  163000    91.019656     2000    2.9868352 
-  164000    91.776359     2000    2.9195788 
-  165000    92.536374     2000    2.5637813 
-  166000    93.296332     2000    2.5553272 
-  167000     94.05653     2000    2.0752912 
-  168000    94.814559     2000    1.9689845 
-  169000    95.576005     2000    1.9117916 
-  170000    96.337863     2000    1.8568914 
-Loop time of 96.3379 on 1 procs for 150000 steps with 2000 atoms
-
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 37.121     | 37.121     | 37.121     |   0.0 | 38.53
-Neigh   | 0.8454     | 0.8454     | 0.8454     |   0.0 |  0.88
-Comm    | 0.11506    | 0.11506    | 0.11506    |   0.0 |  0.12
-Output  | 0.004431   | 0.004431   | 0.004431   |   0.0 |  0.00
-Modify  | 56.517     | 56.517     | 56.517     |   0.0 | 58.67
-Other   |            | 1.735      |            |       |  1.80
-
-Nlocal:    2000 ave 2000 max 2000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    15524 ave 15524 max 15524 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15524
-Ave neighs/atom = 7.762
-Neighbor list builds = 388
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region	  	cylreg delete
-region		hopreg delete
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
-
-region		hopreg union 2 cylreg conereg
-
-unfix		hopper3
-fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run		100000
-Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes
-Step CPU Atoms KinEng 
-  170000            0     2000    1.8568914 
-  171000   0.75704765     2000    2.4011583 
-  172000    1.5101345     2000     3.176628 
-  173000    2.2556529     2000    4.5364486 
-  174000    2.9946566     2000    6.5494125 
-  175000    3.7253478     2000    9.1934319 
-  176000    4.4570525     2000     12.25765 
-  177000    5.1876664     2000    15.799657 
-  178000    5.9178619     2000    19.982558 
-  179000    6.6439464     2000    24.927165 
-  180000    7.3749168     2000    30.428362 
-  181000    8.1011977     2000     36.74232 
-  182000    8.8207343     2000    43.820448 
-  183000    9.5397925     2000    50.903222 
-  184000    10.253098     2000    59.425781 
-  185000    10.965505     2000    69.143119 
-  186000    11.673319     2000    79.210705 
-  187000    12.373966     2000    90.411346 
-  188000    13.075475     2000    102.35389 
-  189000    13.770632     2000    114.93888 
-  190000    14.469445     2000    128.63341 
-  191000    15.158381     2000    143.44526 
-  192000    15.846267     2000    159.04574 
-  193000    16.527754     2000     174.3114 
-  194000    17.204808     2000    190.42123 
-  195000    17.881059     2000    207.70459 
-  196000    18.556555     2000    224.90931 
-  197000    19.229818     2000    242.64914 
-  198000    19.905086     2000    261.48312 
-  199000    20.578518     2000    281.28308 
-  200000     21.25632     2000    302.95108 
-  201000    21.921347     2000    325.95534 
-  202000    22.583873     2000     350.6874 
-  203000    23.244724     2000    376.31773 
-  204000    23.904842     2000    404.21947 
-  205000    24.562788     2000    432.96116 
-  206000    25.217762     2000     462.4113 
-  207000    25.875814     2000    491.91207 
-  208000    26.531285     2000    522.15395 
-  209000    27.184766     2000     553.1024 
-  210000    27.842961     2000     585.7133 
-  211000    28.489339     2000    619.96357 
-  212000    29.139612     2000    653.96189 
-  213000    29.783866     2000     689.8027 
-  214000    30.426881     2000    727.28401 
-  215000     31.06706     2000    766.40354 
-  216000    31.706399     2000    805.65433 
-  217000    32.343033     2000    845.40981 
-  218000    32.989384     2000    884.24637 
-  219000    33.633664     2000     923.5998 
-  220000    34.285172     2000    965.01779 
-  221000    34.931959     2000    1009.1763 
-  222000    35.571624     2000    1054.7789 
-  223000    36.207868     2000    1101.9922 
-  224000    36.836062     2000    1151.1205 
-  225000    37.464514     2000    1201.3979 
-  226000     38.09746     2000    1252.4054 
-  227000    38.732507     1999    1296.6784 
-  228000    39.371367     1997    1342.3466 
-  229000    40.012553     1992    1368.8559 
-  230000    40.652111     1977    1360.2259 
-  231000    41.275478     1965    1340.3793 
-  232000    41.892734     1953    1318.8318 
-  233000     42.50588     1938    1295.5667 
-  234000    43.121427     1924    1270.0641 
-  235000    43.740727     1914     1258.296 
-  236000    44.359241     1902    1224.3945 
-  237000    44.979463     1899    1248.3905 
-  238000    45.597358     1885    1206.9229 
-  239000    46.210114     1875    1195.5429 
-  240000    46.818148     1861    1142.6591 
-  241000    47.411079     1851    1131.5523 
-  242000    48.002522     1841    1116.8741 
-  243000    48.594254     1830    1099.9978 
-  244000    49.191798     1822    1078.6068 
-  245000    49.791332     1814    1072.1498 
-  246000    50.389728     1803    1020.7842 
-  247000    50.984212     1794    1000.1936 
-  248000    51.571047     1781    942.02462 
-  249000    52.149428     1772    916.83697 
-  250000    52.726202     1758    825.10751 
-  251000     53.29913     1748    789.06351 
-  252000    53.871912     1739    753.92258 
-  253000    54.441009     1729    697.83686 
-  254000    55.010203     1718    648.98541 
-  255000    55.573602     1710    620.38129 
-  256000    56.134709     1705    622.43466 
-  257000    56.701827     1700    595.79102 
-  258000    57.264463     1698    608.49223 
-  259000    57.827817     1695     614.0119 
-  260000    58.398994     1690    601.50438 
-  261000    58.964611     1687     608.5892 
-  262000    59.526765     1683    597.07884 
-  263000    60.082729     1682    618.65041 
-  264000    60.640105     1678    615.47784 
-  265000    61.195717     1675    605.27658 
-  266000    61.751087     1671    583.69853 
-  267000    62.305546     1669    600.11043 
-  268000     62.86105     1666    598.79807 
-  269000    63.417551     1663    588.40338 
-  270000    63.974486     1660    579.59387 
-Loop time of 63.9745 on 1 procs for 100000 steps with 1660 atoms
-
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 26.514     | 26.514     | 26.514     |   0.0 | 41.44
-Neigh   | 0.60324    | 0.60324    | 0.60324    |   0.0 |  0.94
-Comm    | 0.075881   | 0.075881   | 0.075881   |   0.0 |  0.12
-Output  | 0.0029137  | 0.0029137  | 0.0029137  |   0.0 |  0.00
-Modify  | 35.686     | 35.686     | 35.686     |   0.0 | 55.78
-Other   |            | 1.092      |            |       |  1.71
-
-Nlocal:    1660 ave 1660 max 1660 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    11681 ave 11681 max 11681 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 11681
-Ave neighs/atom = 7.03675
-Neighbor list builds = 249
-Dangerous builds = 0
-Total wall time: 0:02:48

examples/granregion/log.27Nov18.granregion.funnel.g++.4

@@ -1,601 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable	name string funnel_pour
-
-thermo_modify	flush yes
-units 		si
-variable	PI equal 3.141592653589
-variable	seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	xlo equal 10
-variable	xhi equal 40
-variable	ylo equal 10
-variable	yhi equal 40
-variable	zlo equal -20
-variable	zhi equal 50
-
-variable	xc equal 25
-variable	yc equal 25
-
-variable	zconehi equal 50
-variable	zconelo equal 10
-variable	zcyllo equal 0
-variable	radconelo equal 2
-variable	radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable 	skin equal ${rhi}
-variable 	skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	density equal 1.0
-variable	EYoung equal 10^5
-variable 	Poisson equal 2.0/7.0
-variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+0.285714285714286))
-
-variable	gravity equal 1.0
-
-variable	reff equal 0.5*(${rhi}+${rlo})
-variable	reff equal 0.5*(0.5+${rlo})
-variable	reff equal 0.5*(0.5+0.25)
-variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable        kt equal 4.0*${GShear}/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable	a equal (-2.0*log(${coeffRes})/${PI})^2
-variable	a equal (-2.0*log(0.1)/${PI})^2
-variable	a equal (-2.0*log(0.1)/3.141592653589)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 903.503751814138*0.5
-
-variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable	dt equal ${tcol}*0.05
-variable	dt equal 0.00210943016014969*0.05
-timestep	${dt}
-timestep	0.000105471508007485
-
-###############################################
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		off
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 -20 ${zhi}
-region		boxreg block 10 40 10 40 -20 50
-create_box	1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
-  1 by 1 by 4 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} bin
-neighbor        0.5 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0
-  ghost atom cutoff = 0
-  binsize = 30, bins = 1 1 3
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
-
-region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
-region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
-
-region		hopreg union 2 conereg cylreg
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-
-fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 6.05 | 6.05 | 6.05 Mbytes
-Step CPU Atoms KinEng 
-       0            0        0           -0 
-    1000   0.63366675     2000           -0 
-    2000    1.0221362     2000           -0 
-    3000    1.3905275     2000           -0 
-    4000    1.7514329     2000           -0 
-    5000    2.1040537     2000           -0 
-    6000    2.4468088     2000           -0 
-    7000    2.7853072     2000           -0 
-    8000    3.1109948     2000           -0 
-    9000    3.4281557     2000           -0 
-   10000    3.7435207     2000           -0 
-   11000    3.8612552     2000           -0 
-   12000    3.9786677     2000           -0 
-   13000    4.0988154     2000           -0 
-   14000    4.2249811     2000           -0 
-   15000    4.3562138     2000           -0 
-   16000    4.4940333     2000           -0 
-   17000    4.6394637     2000           -0 
-   18000    4.7909062     2000           -0 
-   19000    4.9482198     2000           -0 
-   20000    5.1116607     2000           -0 
-Loop time of 5.11176 on 4 procs for 20000 steps with 2000 atoms
-
-97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.050997   | 0.14884    | 0.36048    |  32.0 |  2.91
-Neigh   | 0.01374    | 0.025199   | 0.043743   |   7.0 |  0.49
-Comm    | 0.063387   | 0.1781     | 0.29748    |  22.6 |  3.48
-Output  | 0.0016627  | 0.0060938  | 0.015082   |   6.8 |  0.12
-Modify  | 1.1198     | 1.987      | 3.7195     |  72.6 | 38.87
-Other   |            | 2.767      |            |       | 54.12
-
-Nlocal:    500 ave 505 max 493 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    159.25 ave 254 max 71 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    397.5 ave 616 max 214 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 1590
-Ave neighs/atom = 0.795
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Per MPI rank memory allocation (min/avg/max) = 12.37 | 12.51 | 12.7 Mbytes
-Step CPU Atoms KinEng 
-   20000            0     2000    6443.7665 
-   21000   0.11261106     2000    6572.3531 
-   22000   0.23091817     2000    6723.8376 
-   23000   0.35577631     2000    6853.1812 
-   24000   0.48790455     2000    6976.0209 
-   25000   0.63509274     2000    7096.9955 
-   26000   0.78251743     2000    7215.5795 
-   27000   0.93707466     2000    7349.2382 
-   28000    1.1032445     2000    7471.8719 
-   29000    1.2721858     2000    7574.8228 
-   30000     1.449265     2000    7659.3836 
-   31000    1.5742557     2000    7703.6856 
-   32000    1.7076068     2000     7644.279 
-   33000    1.8527873     2000    7526.6944 
-   34000     2.009855     2000    7370.0821 
-   35000    2.1766446     2000    7193.0459 
-   36000    2.3557482     2000    6990.9912 
-   37000    2.5468907     2000     6849.286 
-   38000    2.7480681     2000    6701.7548 
-   39000    2.9574037     2000    6538.6915 
-   40000    3.1807711     2000    6382.3209 
-   41000    3.3486595     2000     6216.424 
-   42000    3.5162592     2000      6091.29 
-   43000     3.687057     2000    5945.3256 
-   44000    3.8662596     2000     5840.875 
-   45000    4.0557241     2000     5649.763 
-   46000    4.2541051     2000    5476.2837 
-   47000    4.4571214     2000    5277.0701 
-   48000    4.6628008     2000    5123.9796 
-   49000    4.8686502     2000    4968.3344 
-   50000    5.0788848     2000    4869.5754 
-   51000    5.2552598     2000    4704.8517 
-   52000    5.4428713     2000    4522.8978 
-   53000    5.6520596     2000    4393.8047 
-   54000    5.8613031     2000     4235.438 
-   55000    6.0776098     2000    4082.3073 
-   56000    6.2998042     2000    3901.0483 
-   57000    6.5321434     2000    3718.0882 
-   58000    6.7745438     2000     3504.621 
-   59000    7.0237701     2000    3285.7484 
-   60000    7.2791855     2000    3047.3386 
-   61000     7.489058     2000    2875.4032 
-   62000    7.7044094     2000      2647.83 
-   63000    7.9194827     2000    2396.5343 
-   64000    8.1429474     2000    2107.2113 
-   65000    8.3745618     2000    1858.1977 
-   66000     8.610673     2000    1615.8096 
-   67000    8.8505244     2000    1416.5065 
-   68000    9.0955915     2000    1206.8534 
-   69000    9.3609676     2000    953.93974 
-   70000    9.6382594     2000     766.9148 
-   71000    9.8719468     2000    611.45063 
-   72000    10.095534     2000    464.94805 
-   73000    10.317962     2000    364.31415 
-   74000    10.547287     2000    298.77524 
-   75000    10.764052     2000    245.73022 
-   76000    10.978769     2000     207.8035 
-   77000    11.199921     2000     179.1305 
-   78000    11.410296     2000    151.21032 
-   79000    11.624499     2000    124.49675 
-   80000    11.849562     2000    106.71504 
-   81000    12.077449     2000    93.299034 
-   82000    12.306904     2000    81.220408 
-   83000    12.539016     2000    67.383955 
-   84000    12.773108     2000    57.287165 
-   85000    13.009487     2000    49.255887 
-   86000    13.252544     2000    44.082536 
-   87000    13.502564     2000    40.193574 
-   88000    13.747198     2000    36.903867 
-   89000    13.993028     2000     33.55332 
-   90000    14.240036     2000    30.730912 
-   91000    14.472719     2000    28.650574 
-   92000    14.708542     2000    26.377609 
-   93000    14.948106     2000    24.433165 
-   94000    15.186653     2000    22.933076 
-   95000    15.428022     2000     22.31788 
-   96000    15.676323     2000    20.829124 
-   97000    15.916326     2000    19.401354 
-   98000    16.160197     2000    18.943699 
-   99000    16.404796     2000    17.690599 
-  100000    16.659731     2000    17.215943 
-  101000    16.904498     2000    15.948087 
-  102000    17.150993     2000    15.140324 
-  103000     17.39584     2000    14.885674 
-  104000    17.643707     2000    14.414752 
-  105000    17.889343     2000    14.270676 
-  106000    18.136159     2000    13.943799 
-  107000    18.383653     2000    13.840145 
-  108000    18.630952     2000    12.826341 
-  109000    18.878218     2000    12.209012 
-  110000    19.125558     2000    11.916194 
-  111000      19.3726     2000    11.970849 
-  112000    19.621494     2000     11.56909 
-  113000    19.869978     2000    11.390562 
-  114000    20.123402     2000    11.276545 
-  115000    20.370963     2000    11.171298 
-  116000    20.619975     2000    11.686225 
-  117000    20.869585     2000    11.379805 
-  118000    21.118875     2000    10.539511 
-  119000     21.36837     2000    10.064595 
-  120000    21.629511     2000    10.003722 
-  121000    21.877867     2000    9.6974586 
-  122000    22.127922     2000    9.7156209 
-  123000    22.378215     2000     9.615256 
-  124000    22.630463     2000    8.8979008 
-  125000    22.882154     2000    8.2220003 
-  126000    23.135763     2000    8.3153866 
-  127000    23.392389     2000    8.0945497 
-  128000    23.645521     2000    7.8942467 
-  129000     23.89965     2000    7.4794776 
-  130000    24.153195     2000    7.3635341 
-  131000    24.406239     2000    7.5757743 
-  132000     24.66016     2000    7.7047492 
-  133000    24.914093     2000    8.0142133 
-  134000    25.173429     2000    8.1716714 
-  135000    25.433318     2000    7.7803343 
-  136000    25.692997     2000    6.3545482 
-  137000    25.947787     2000     6.313769 
-  138000    26.200427     2000    6.4948596 
-  139000    26.452514     2000    6.6183259 
-  140000    26.714963     2000    6.7922281 
-  141000    26.968235     2000    7.0752448 
-  142000    27.220962     2000    7.2328717 
-  143000    27.474819     2000     7.626453 
-  144000    27.728029     2000    7.4576787 
-  145000    27.981958     2000     7.124435 
-  146000    28.236591     2000    7.2581589 
-  147000    28.489842     2000    7.0622049 
-  148000    28.744432     2000    7.1672801 
-  149000    28.998739     2000    7.3248363 
-  150000    29.253511     2000    7.0092266 
-  151000     29.50567     2000    6.8124438 
-  152000    29.759836     2000    6.9808705 
-  153000    30.015359     2000    7.1516731 
-  154000    30.275488     2000    6.6245443 
-  155000    30.533407     2000    5.5867165 
-  156000    30.788683     2000     5.318949 
-  157000    31.043126     2000    5.1195805 
-  158000    31.297011     2000    5.2045485 
-  159000    31.551327     2000      5.24992 
-  160000    31.807728     2000    5.3270577 
-  161000    32.061371     2000     4.995281 
-  162000    32.315467     2000    5.0755874 
-  163000     32.57628     2000    5.0788135 
-  164000     32.83119     2000    4.5917317 
-  165000    33.085634     2000    4.6255452 
-  166000    33.344148     2000    4.2563299 
-  167000    33.599342     2000    3.3808566 
-  168000    33.853488     2000     3.218931 
-  169000    34.121464     2000    3.0839289 
-  170000    34.378727     2000    3.0358838 
-Loop time of 34.3788 on 4 procs for 150000 steps with 2000 atoms
-
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.5861     | 10.058     | 12.152     |  68.4 | 29.26
-Neigh   | 0.17612    | 0.25274    | 0.30005    |   9.2 |  0.74
-Comm    | 1.5024     | 2.6626     | 3.4174     |  44.9 |  7.74
-Output  | 0.006542   | 0.019532   | 0.046425   |  11.5 |  0.06
-Modify  | 11.945     | 14.674     | 16.29      |  42.7 | 42.68
-Other   |            | 6.711      |            |       | 19.52
-
-Nlocal:    500 ave 508 max 489 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Nghost:    446.75 ave 708 max 191 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    4498 ave 5441 max 3786 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 17992
-Ave neighs/atom = 8.996
-Neighbor list builds = 403
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region	  	cylreg delete
-region		hopreg delete
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
-
-region		hopreg union 2 cylreg conereg
-
-unfix		hopper3
-fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run		100000
-Per MPI rank memory allocation (min/avg/max) = 13.68 | 15.35 | 16.59 Mbytes
-Step CPU Atoms KinEng 
-  170000            0     2000    3.0358838 
-  171000   0.25455499     2000    3.7725185 
-  172000   0.50768304     2000     4.727285 
-  173000   0.76122355     2000    5.9840449 
-  174000    1.0141416     2000    8.0335022 
-  175000    1.2750733     2000    10.177259 
-  176000    1.5277736     2000    13.655163 
-  177000    1.7810826     2000    17.987975 
-  178000    2.0348532     2000    23.266471 
-  179000    2.2915859     2000    29.266364 
-  180000     2.547174     2000     35.84089 
-  181000    2.8009758     2000    43.130989 
-  182000    3.0531759     2000    51.177142 
-  183000    3.3130636     2000    60.031831 
-  184000    3.5651338     2000     69.52374 
-  185000    3.8185399     2000    79.941907 
-  186000     4.070199     2000    91.195382 
-  187000    4.3204038     2000     102.1696 
-  188000    4.5699775     2000    112.73657 
-  189000    4.8184452     2000    123.57252 
-  190000    5.0653601     2000    135.59942 
-  191000    5.3119307     2000    147.37757 
-  192000    5.5574484     2000    159.12931 
-  193000    5.8029084     2000    170.90271 
-  194000    6.0463562     2000    185.71189 
-  195000    6.2883332     2000    201.83733 
-  196000    6.5281694     2000    218.30785 
-  197000    6.7682493     2000    236.05694 
-  198000    7.0084231     2000    255.23099 
-  199000    7.2519951     2000    273.94566 
-  200000    7.5010133     2000    293.91107 
-  201000    7.7396591     2000    316.52142 
-  202000    7.9784184     2000    340.91391 
-  203000     8.224021     2000    364.81801 
-  204000    8.4597676     2000    390.06478 
-  205000    8.6934731     2000    415.90918 
-  206000    8.9342225     2000     441.0995 
-  207000    9.1714027     2000    467.40314 
-  208000    9.4081488     2000    494.93631 
-  209000    9.6457636     2000    524.70539 
-  210000    9.8831718     2000    556.52058 
-  211000    10.118018     2000    589.36821 
-  212000      10.3541     2000     622.6887 
-  213000    10.587226     2000    657.05888 
-  214000    10.820744     2000    691.14292 
-  215000    11.055785     2000    726.94959 
-  216000    11.298702     2000    762.92802 
-  217000    11.534793     2000    801.23648 
-  218000    11.769849     2000     841.1559 
-  219000    12.000917     2000     882.4342 
-  220000    12.232812     2000     924.8466 
-  221000    12.461166     2000    968.86229 
-  222000    12.698451     2000    1013.1381 
-  223000    12.930287     2000    1058.2988 
-  224000    13.172862     2000    1105.2911 
-  225000    13.405001     2000    1152.8617 
-  226000    13.633187     1999    1197.6777 
-  227000    13.857126     1998    1243.1211 
-  228000    14.079622     1992    1262.1402 
-  229000    14.303362     1987    1281.9162 
-  230000    14.530392     1973    1264.0674 
-  231000    14.756486     1964    1277.8347 
-  232000    14.984495     1953    1266.7926 
-  233000    15.213102     1940    1244.0038 
-  234000    15.441666     1925    1206.4472 
-  235000    15.667547     1914      1193.33 
-  236000    15.895047     1901    1160.4096 
-  237000    16.120833     1890    1141.6816 
-  238000    16.346628     1883    1149.1584 
-  239000    16.573303     1877    1141.7514 
-  240000    16.801035     1871    1146.8662 
-  241000    17.024775     1866     1152.561 
-  242000    17.248651     1858    1148.2529 
-  243000     17.47241     1847    1114.7239 
-  244000     17.70222     1832    1070.9996 
-  245000    17.926477     1824    1066.7549 
-  246000    18.157588     1813    1027.1865 
-  247000    18.378868     1804    1011.5024 
-  248000    18.599988     1797    993.10451 
-  249000    18.819007     1787    951.89778 
-  250000    19.044634     1777    926.30475 
-  251000    19.254408     1764    875.07091 
-  252000    19.465788     1755    824.89358 
-  253000    19.676327     1742    742.51957 
-  254000    19.887648     1731    708.30958 
-  255000    20.094912     1722    690.09761 
-  256000    20.299963     1713    638.00218 
-  257000    20.506153     1705    596.86839 
-  258000    20.713994     1701    583.71937 
-  259000    20.919755     1691     549.0049 
-  260000    21.123122     1688     549.4278 
-  261000    21.332215     1684    535.35719 
-  262000    21.533673     1682    546.74031 
-  263000    21.737042     1678    532.69324 
-  264000    21.941306     1676    537.89254 
-  265000     22.15135     1676    559.50898 
-  266000    22.358371     1670    540.21452 
-  267000    22.563236     1668    557.19857 
-  268000    22.764648     1665    569.52869 
-  269000     22.96391     1658    543.77057 
-  270000    23.172415     1656    550.23716 
-Loop time of 23.1725 on 4 procs for 100000 steps with 1656 atoms
-
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.3849     | 7.3002     | 10.192     |  91.3 | 31.50
-Neigh   | 0.14271    | 0.16781    | 0.19054    |   4.5 |  0.72
-Comm    | 1.086      | 1.9721     | 2.6157     |  42.7 |  8.51
-Output  | 0.0018437  | 0.013918   | 0.041359   |  13.5 |  0.06
-Modify  | 8.6598     | 9.3198     | 9.8874     |  16.6 | 40.22
-Other   |            | 4.399      |            |       | 18.98
-
-Nlocal:    414 ave 454 max 385 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost:    395.25 ave 645 max 157 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    3498.5 ave 4524 max 2034 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 13994
-Ave neighs/atom = 8.45048
-Neighbor list builds = 240
-Dangerous builds = 0
-Total wall time: 0:01:02

examples/granregion/log.27Nov18.granregion.mixer.g++.1

@@ -1,602 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-variable	name string mixer
-
-thermo_modify	flush yes
-variable	seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable	rlo equal 0.3
-variable	rhi equal 0.6
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.3
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.6
-variable 	skin equal ${rhi}
-variable 	skin equal 0.6
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	kn equal 10^5
-variable	kt equal 0.2*${kn}
-variable	kt equal 0.2*100000
-
-variable	gravity equal 1.0
-variable	density equal 1.0
-
-variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable	a equal (-2.0*log(${coeffRes})/PI)^2
-variable	a equal (-2.0*log(0.1)/PI)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 806.699778405191*0.5
-
-variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable	dt equal ${tcol}*0.02
-variable	dt equal 0.00236257621510454*0.02
-timestep	${dt}
-timestep	4.72515243020908e-05
-
-###############################################
-
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		on
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block 0 20 0 20 0 20
-create_box	1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} bin
-neighbor        0.6 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0
-  ghost atom cutoff = 0
-  binsize = 20, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region	     	insreg cylinder z 10 10 8 10 18 side in units box
-region	    	cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable	theta equal (step/400000)*2*PI
-
-region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
-region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
-
-region		mixer intersect 3 cylreg b1 b2 side in
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
-thermo_modify	flush yes lost warn
-
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes
-Step CPU Atoms KinEng v_theta 
-       0            0        0           -0            0 
-    1000   0.15327144      444           -0  0.015707963 
-    2000   0.30070925      444           -0  0.031415927 
-    3000   0.44653535      444           -0   0.04712389 
-    4000   0.59226131      444           -0  0.062831853 
-    5000   0.73794818      444           -0  0.078539816 
-    6000   0.88327622      444           -0   0.09424778 
-    7000    1.0286083      444           -0   0.10995574 
-    8000    1.1740625      444           -0   0.12566371 
-    9000    1.3224797      444           -0   0.14137167 
-   10000    1.4717772      444           -0   0.15707963 
-   11000    1.6204555      444           -0    0.1727876 
-   12000    1.7690799      444           -0   0.18849556 
-   13000     1.918304      444           -0   0.20420352 
-   14000    2.0670426      444           -0   0.21991149 
-   15000    2.2157068      444           -0   0.23561945 
-   16000    2.3642888      444           -0   0.25132741 
-   17000    2.5129776      444           -0   0.26703538 
-   18000    2.6614521      444           -0   0.28274334 
-   19000    2.8100598      444           -0    0.2984513 
-   20000    2.9591351      444           -0   0.31415927 
-   21000    3.1073661      444           -0   0.32986723 
-   22000    3.2557554      444           -0   0.34557519 
-   23000    3.4041324      444           -0   0.36128316 
-   24000    3.5526814      444           -0   0.37699112 
-   25000     3.700824      444           -0   0.39269908 
-   26000    3.8496137      444           -0   0.40840704 
-   27000    3.9986103      444           -0   0.42411501 
-   28000    4.1475384      444           -0   0.43982297 
-   29000    4.2963772      444           -0   0.45553093 
-   30000    4.4454341      444           -0    0.4712389 
-   31000    4.5942066      444           -0   0.48694686 
-   32000    4.7434044      444           -0   0.50265482 
-   33000     4.893549      444           -0   0.51836279 
-   34000    5.0427935      444           -0   0.53407075 
-   35000    5.1920972      444           -0   0.54977871 
-   36000    5.3411844      444           -0   0.56548668 
-   37000    5.4904606      444           -0   0.58119464 
-   38000    5.6397707      444           -0    0.5969026 
-   39000    5.7900345      444           -0   0.61261057 
-   40000    5.9405882      444           -0   0.62831853 
-   41000     6.089345      444           -0   0.64402649 
-   42000    6.2388933      444           -0   0.65973446 
-   43000    6.3888056      444           -0   0.67544242 
-   44000    6.5379841      444           -0   0.69115038 
-   45000    6.6875141      444           -0   0.70685835 
-   46000    6.8370855      444           -0   0.72256631 
-   47000    6.9866009      444           -0   0.73827427 
-   48000    7.1364653      444           -0   0.75398224 
-   49000    7.2859883      444           -0    0.7696902 
-   50000    7.4368248      444           -0   0.78539816 
-   51000    7.5870779      444           -0   0.80110613 
-   52000    7.7370813      444           -0   0.81681409 
-   53000    7.8879561      444           -0   0.83252205 
-   54000    8.0383027      444           -0   0.84823002 
-   55000    8.1916294      444           -0   0.86393798 
-   56000    8.3458471      444           -0   0.87964594 
-   57000    8.5010631      444           -0   0.89535391 
-   58000    8.6560545      444           -0   0.91106187 
-   59000    8.8110209      444           -0   0.92676983 
-   60000    8.9674675      444           -0    0.9424778 
-   61000    9.1231239      444           -0   0.95818576 
-   62000    9.2785382      444           -0   0.97389372 
-   63000    9.4343674      444           -0   0.98960169 
-   64000    9.5911541      444           -0    1.0053096 
-   65000    9.7477772      444           -0    1.0210176 
-   66000    9.9050307      444           -0    1.0367256 
-   67000    10.063978      444           -0    1.0524335 
-   68000    10.221835      444           -0    1.0681415 
-   69000     10.37944      444           -0    1.0838495 
-   70000    10.537409      444           -0    1.0995574 
-   71000    10.695649      444           -0    1.1152654 
-   72000     10.85453      444           -0    1.1309734 
-   73000    11.013438      444           -0    1.1466813 
-   74000    11.172689      444           -0    1.1623893 
-   75000    11.332172      444           -0    1.1780972 
-   76000    11.492824      444           -0    1.1938052 
-   77000    11.653915      444           -0    1.2095132 
-   78000    11.815798      444           -0    1.2252211 
-   79000     11.97868      444           -0    1.2409291 
-   80000    12.141392      444           -0    1.2566371 
-   81000     12.30536      444           -0     1.272345 
-   82000    12.468797      444           -0     1.288053 
-   83000    12.633028      444           -0     1.303761 
-   84000    12.797936      444           -0    1.3194689 
-   85000    13.019726      888           -0    1.3351769 
-   86000    13.333436      888           -0    1.3508848 
-   87000    13.648179      888           -0    1.3665928 
-   88000    13.962435      888           -0    1.3823008 
-   89000    14.276158      888           -0    1.3980087 
-   90000    14.590669      888           -0    1.4137167 
-   91000    14.904268      888           -0    1.4294247 
-   92000    15.216788      888           -0    1.4451326 
-   93000    15.529868      888           -0    1.4608406 
-   94000    15.843157      888           -0    1.4765485 
-   95000    16.156564      888           -0    1.4922565 
-   96000    16.469569      888           -0    1.5079645 
-   97000    16.784048      888           -0    1.5236724 
-   98000    17.100451      888           -0    1.5393804 
-   99000    17.416338      888           -0    1.5550884 
-  100000    17.733482      888           -0    1.5707963 
-  101000    18.052522      888           -0    1.5865043 
-  102000    18.371428      888           -0    1.6022123 
-  103000    18.690222      888           -0    1.6179202 
-  104000    19.009665      888           -0    1.6336282 
-  105000    19.328189      888           -0    1.6493361 
-  106000    19.647804      888           -0    1.6650441 
-  107000     19.96805      888           -0    1.6807521 
-  108000    20.286857      888           -0      1.69646 
-  109000    20.607965      888           -0     1.712168 
-  110000    20.931749      888           -0     1.727876 
-  111000    21.251903      888           -0    1.7435839 
-  112000    21.572158      888           -0    1.7592919 
-  113000    21.892612      888           -0    1.7749998 
-  114000    22.214408      888           -0    1.7907078 
-  115000    22.535498      888           -0    1.8064158 
-  116000    22.856752      888           -0    1.8221237 
-  117000    23.178885      888           -0    1.8378317 
-  118000    23.501127      888           -0    1.8535397 
-  119000      23.8241      888           -0    1.8692476 
-  120000    24.147258      888           -0    1.8849556 
-  121000    24.472969      888           -0    1.9006636 
-  122000    24.799108      888           -0    1.9163715 
-  123000    25.125275      888           -0    1.9320795 
-  124000    25.453866      888           -0    1.9477874 
-  125000    25.784766      888           -0    1.9634954 
-  126000    26.117013      888           -0    1.9792034 
-  127000    26.448734      888           -0    1.9949113 
-  128000    26.780032      888           -0    2.0106193 
-  129000    27.113678      888           -0    2.0263273 
-  130000    27.450001      888           -0    2.0420352 
-  131000    27.782047      888           -0    2.0577432 
-  132000    28.114287      888           -0    2.0734512 
-  133000    28.446648      888           -0    2.0891591 
-  134000    28.780438      888           -0    2.1048671 
-  135000    29.116443      888           -0     2.120575 
-  136000    29.451848      888           -0     2.136283 
-  137000    29.787778      888           -0     2.151991 
-  138000     30.12804      888           -0    2.1676989 
-  139000     30.46814      888           -0    2.1834069 
-  140000    30.808946      888           -0    2.1991149 
-  141000    31.147584      888           -0    2.2148228 
-  142000    31.486475      888           -0    2.2305308 
-  143000    31.826754      888           -0    2.2462387 
-  144000    32.165796      888           -0    2.2619467 
-  145000    32.506074      888           -0    2.2776547 
-  146000    32.847604      888           -0    2.2933626 
-  147000    33.188988      888           -0    2.3090706 
-  148000    33.532869      888           -0    2.3247786 
-  149000    33.876629      888           -0    2.3404865 
-  150000    34.221172      888           -0    2.3561945 
-  151000    34.562559      888           -0    2.3719025 
-  152000    34.904679      888           -0    2.3876104 
-  153000    35.247727      888           -0    2.4033184 
-  154000    35.591228      888           -0    2.4190263 
-  155000    35.949192      888           -0    2.4347343 
-  156000    36.320157      888           -0    2.4504423 
-  157000    36.693571      888           -0    2.4661502 
-  158000    37.069463      888           -0    2.4818582 
-  159000     37.44221      888           -0    2.4975662 
-  160000     37.81863      888           -0    2.5132741 
-  161000    38.195121      888           -0    2.5289821 
-  162000    38.573424      888           -0      2.54469 
-  163000    38.950044      888           -0     2.560398 
-  164000    39.331977      888           -0     2.576106 
-  165000    39.714367      888           -0    2.5918139 
-  166000    40.097099      888           -0    2.6075219 
-  167000    40.477443      888           -0    2.6232299 
-  168000    40.860404      888           -0    2.6389378 
-  169000    41.244357      888           -0    2.6546458 
-  170000    41.658126     1000           -0    2.6703538 
-  171000    42.082517     1000           -0    2.6860617 
-  172000    42.507502     1000           -0    2.7017697 
-  173000     42.93363     1000           -0    2.7174776 
-  174000    43.361133     1000           -0    2.7331856 
-  175000    43.792381     1000           -0    2.7488936 
-  176000    44.223827     1000           -0    2.7646015 
-  177000    44.656581     1000           -0    2.7803095 
-  178000    45.087615     1000           -0    2.7960175 
-  179000    45.521129     1000           -0    2.8117254 
-  180000    45.957808     1000           -0    2.8274334 
-  181000    46.391451     1000           -0    2.8431414 
-  182000    46.825486     1000           -0    2.8588493 
-  183000     47.26091     1000           -0    2.8745573 
-  184000    47.694263     1000           -0    2.8902652 
-  185000    48.123312     1000           -0    2.9059732 
-  186000    48.554081     1000           -0    2.9216812 
-  187000    48.982617     1000           -0    2.9373891 
-  188000    49.414355     1000           -0    2.9530971 
-  189000     49.84753     1000           -0    2.9688051 
-  190000    50.284462     1000           -0     2.984513 
-  191000     50.71899     1000           -0     3.000221 
-  192000    51.157278     1000           -0    3.0159289 
-  193000    51.586171     1000           -0    3.0316369 
-  194000    52.011691     1000           -0    3.0473449 
-  195000    52.437732     1000           -0    3.0630528 
-  196000    52.863703     1000           -0    3.0787608 
-  197000    53.290403     1000           -0    3.0944688 
-  198000      53.7191     1000           -0    3.1101767 
-  199000    54.147195     1000           -0    3.1258847 
-  200000    54.575967     1000           -0    3.1415927 
-Loop time of 54.576 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 14960.907 tau/day, 3664.615 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.7989     | 3.7989     | 3.7989     |   0.0 |  6.96
-Neigh   | 0.067629   | 0.067629   | 0.067629   |   0.0 |  0.12
-Comm    | 0.63734    | 0.63734    | 0.63734    |   0.0 |  1.17
-Output  | 0.0049303  | 0.0049303  | 0.0049303  |   0.0 |  0.01
-Modify  | 49.1       | 49.1       | 49.1       |   0.0 | 89.97
-Other   |            | 0.9668     |            |       |  1.77
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    196 ave 196 max 196 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    3910 ave 3910 max 3910 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3910
-Ave neighs/atom = 3.91
-Neighbor list builds = 219
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes
-Step CPU Atoms KinEng v_theta 
-  200000            0     1000   0.93873133    3.1415927 
-  201000    0.4261198     1000   0.93239566    3.1573006 
-  202000   0.84928846     1000   0.90333835    3.1730086 
-  203000    1.2720087     1000   0.89351493    3.1887165 
-  204000    1.6929317     1000   0.87648478    3.2044245 
-  205000     2.114043     1000   0.86818482    3.2201325 
-  206000    2.5357664     1000   0.86033251    3.2358404 
-  207000    2.9579847     1000   0.85442625    3.2515484 
-  208000    3.3812878     1000    0.8517451    3.2672564 
-  209000    3.8124611     1000   0.84406987    3.2829643 
-  210000    4.2440236     1000   0.83964642    3.2986723 
-  211000    4.6781921     1000   0.82994066    3.3143802 
-  212000    5.1116509     1000   0.82908369    3.3300882 
-  213000    5.5468135     1000   0.83115482    3.3457962 
-  214000    5.9802556     1000   0.82680518    3.3615041 
-  215000    6.4107294     1000    0.8223909    3.3772121 
-  216000    6.8419023     1000   0.81872537    3.3929201 
-  217000    7.2763367     1000   0.82446065     3.408628 
-  218000    7.7160695     1000   0.82278874     3.424336 
-  219000    8.1540956     1000   0.83017397     3.440044 
-  220000    8.5917952     1000   0.82232305    3.4557519 
-  221000    9.0296218     1000   0.82584132    3.4714599 
-  222000    9.4719794     1000   0.82143909    3.4871678 
-  223000    9.9180939     1000   0.82925587    3.5028758 
-  224000    10.361852     1000   0.84546265    3.5185838 
-  225000    10.803539     1000   0.84436452    3.5342917 
-  226000    11.248456     1000   0.84849375    3.5499997 
-  227000    11.695092     1000    0.8409057    3.5657077 
-  228000    12.136044     1000   0.83139305    3.5814156 
-  229000    12.579807     1000   0.83098473    3.5971236 
-  230000     13.02219     1000   0.81335147    3.6128316 
-  231000    13.463863     1000   0.78946649    3.6285395 
-  232000    13.906293     1000   0.78807613    3.6442475 
-  233000    14.348807     1000   0.79086655    3.6599554 
-  234000    14.793175     1000   0.79358862    3.6756634 
-  235000    15.238316     1000   0.79444252    3.6913714 
-  236000    15.683342     1000   0.79392156    3.7070793 
-  237000     16.12611     1000   0.80416034    3.7227873 
-  238000      16.5711     1000   0.80365093    3.7384953 
-  239000    17.014355     1000   0.80860323    3.7542032 
-  240000    17.454467     1000   0.80245788    3.7699112 
-  241000     17.89162     1000   0.79602568    3.7856191 
-  242000    18.330859     1000   0.79023692    3.8013271 
-  243000    18.769301     1000   0.79066782    3.8170351 
-  244000    19.211293     1000   0.77671368     3.832743 
-  245000    19.651443     1000   0.77121874     3.848451 
-  246000    20.092102     1000   0.74658977     3.864159 
-  247000    20.532732     1000   0.73825017    3.8798669 
-  248000    20.975646     1000    0.7187986    3.8955749 
-  249000    21.418807     1000   0.71707058    3.9112829 
-  250000    21.862497     1000   0.72983635    3.9269908 
-  251000    22.311832     1000    0.7355358    3.9426988 
-  252000     22.75883     1000   0.74427811    3.9584067 
-  253000    23.203455     1000   0.74968093    3.9741147 
-  254000    23.651472     1000   0.75350303    3.9898227 
-  255000    24.102152     1000   0.75617916    4.0055306 
-  256000    24.554236     1000   0.74949839    4.0212386 
-  257000    25.008718     1000   0.73534118    4.0369466 
-  258000    25.461913     1000   0.73761942    4.0526545 
-  259000    25.916674     1000   0.75485851    4.0683625 
-  260000    26.373941     1000   0.77147511    4.0840704 
-  261000    26.832072     1000   0.76658917    4.0997784 
-  262000     27.28741     1000   0.76441563    4.1154864 
-  263000    27.742157     1000   0.74449444    4.1311943 
-  264000    28.192718     1000    0.7403314    4.1469023 
-  265000    28.642541     1000   0.74262656    4.1626103 
-  266000     29.09406     1000   0.74117022    4.1783182 
-  267000    29.547747     1000   0.73877643    4.1940262 
-  268000    29.998243     1000   0.75062626    4.2097342 
-  269000    30.449751     1000   0.74649396    4.2254421 
-  270000    30.901232     1000   0.75371324    4.2411501 
-  271000    31.354755     1000   0.75254842     4.256858 
-  272000    31.810717     1000   0.74245946     4.272566 
-  273000    32.265754     1000   0.73056023     4.288274 
-  274000    32.719719     1000   0.72004393    4.3039819 
-  275000    33.173929     1000   0.70665742    4.3196899 
-  276000    33.628581     1000   0.69417262    4.3353979 
-  277000    34.080936     1000   0.67343474    4.3511058 
-  278000    34.532053     1000   0.66922758    4.3668138 
-  279000    34.985569     1000   0.66239909    4.3825218 
-  280000    35.443496     1000   0.66406486    4.3982297 
-  281000    35.901536     1000   0.67123654    4.4139377 
-  282000    36.357765     1000   0.67660885    4.4296456 
-  283000    36.811956     1000    0.6809288    4.4453536 
-  284000    37.266937     1000   0.69561154    4.4610616 
-  285000    37.720866     1000   0.70874512    4.4767695 
-  286000    38.177032     1000   0.72957833    4.4924775 
-  287000    38.633109     1000   0.72891066    4.5081855 
-  288000    39.086933     1000   0.72673285    4.5238934 
-  289000    39.538699     1000   0.72583062    4.5396014 
-  290000    39.991294     1000    0.7209406    4.5553093 
-  291000    40.437987     1000   0.70642559    4.5710173 
-  292000    40.885753     1000   0.69074151    4.5867253 
-  293000    41.326601     1000   0.68041469    4.6024332 
-  294000    41.763719     1000    0.6712034    4.6181412 
-  295000    42.198532     1000   0.66140336    4.6338492 
-  296000    42.635139     1000   0.65458145    4.6495571 
-  297000    43.071132     1000   0.63884999    4.6652651 
-  298000    43.507309     1000   0.63182296    4.6809731 
-  299000    43.943936     1000    0.6324286     4.696681 
-  300000    44.383148     1000   0.62640427     4.712389 
-  301000    44.819379     1000   0.62138494    4.7280969 
-  302000    45.260834     1000   0.62902694    4.7438049 
-  303000    45.705719     1000   0.63308052    4.7595129 
-  304000     46.14622     1000   0.63266845    4.7752208 
-  305000    46.586693     1000   0.63464534    4.7909288 
-  306000    47.028768     1000   0.62941378    4.8066368 
-  307000    47.470183     1000   0.62801025    4.8223447 
-  308000    47.914518     1000   0.62291875    4.8380527 
-  309000    48.365654     1000   0.62529494    4.8537606 
-  310000    48.817185     1000   0.62504442    4.8694686 
-  311000    49.269423     1000   0.63074915    4.8851766 
-  312000    49.722869     1000   0.64292914    4.9008845 
-  313000    50.175859     1000   0.65319818    4.9165925 
-  314000    50.630132     1000   0.66755513    4.9323005 
-  315000    51.084836     1000   0.67585436    4.9480084 
-  316000    51.539391     1000   0.67676226    4.9637164 
-  317000    51.995233     1000   0.67394312    4.9794244 
-  318000    52.453581     1000   0.67299959    4.9951323 
-  319000    52.906322     1000   0.68074615    5.0108403 
-  320000    53.362206     1000   0.67696004    5.0265482 
-  321000    53.813824     1000   0.67899008    5.0422562 
-  322000    54.264433     1000   0.67901671    5.0579642 
-  323000    54.715627     1000   0.67620354    5.0736721 
-  324000       55.168     1000   0.67165541    5.0893801 
-  325000    55.620891     1000   0.67820953    5.1050881 
-  326000    56.073685     1000   0.67490808     5.120796 
-  327000    56.526012     1000   0.67238149     5.136504 
-  328000    56.977525     1000   0.66885914     5.152212 
-  329000    57.431088     1000   0.66876389    5.1679199 
-  330000    57.886694     1000   0.66879597    5.1836279 
-  331000    58.338381     1000   0.66577546    5.1993358 
-  332000    58.791084     1000    0.6602875    5.2150438 
-  333000    59.242965     1000   0.65879422    5.2307518 
-  334000    59.698559     1000    0.6581474    5.2464597 
-  335000    60.153261     1000    0.6521249    5.2621677 
-  336000    60.605605     1000   0.63371979    5.2778757 
-  337000    61.059824     1000   0.62373279    5.2935836 
-  338000    61.510606     1000    0.6212013    5.3092916 
-  339000    61.962049     1000   0.62303395    5.3249995 
-  340000    62.413564     1000   0.63183785    5.3407075 
-  341000     62.86366     1000   0.64387158    5.3564155 
-  342000    63.317623     1000   0.65045982    5.3721234 
-  343000    63.772034     1000   0.65401192    5.3878314 
-  344000    64.225206     1000   0.65181077    5.4035394 
-  345000    64.681317     1000   0.64098248    5.4192473 
-  346000    65.136483     1000   0.63163559    5.4349553 
-  347000    65.588996     1000   0.64182161    5.4506633 
-  348000    66.042215     1000   0.65528889    5.4663712 
-  349000    66.501687     1000   0.66603277    5.4820792 
-  350000    66.960896     1000   0.67362185    5.4977871 
-  351000    67.417316     1000   0.68867905    5.5134951 
-  352000    67.876742     1000    0.6907547    5.5292031 
-  353000    68.336836     1000   0.69043981     5.544911 
-  354000    68.797396     1000   0.68676964     5.560619 
-  355000    69.255062     1000   0.68019369     5.576327 
-  356000    69.711663     1000   0.66189875    5.5920349 
-  357000    70.172728     1000   0.65275709    5.6077429 
-  358000    70.632655     1000   0.64560617    5.6234508 
-  359000    71.091165     1000   0.63865266    5.6391588 
-  360000    71.548341     1000    0.6366388    5.6548668 
-  361000    72.006137     1000   0.63619567    5.6705747 
-  362000    72.466621     1000   0.63986167    5.6862827 
-  363000    72.928505     1000     0.656198    5.7019907 
-  364000    73.391876     1000   0.66522563    5.7176986 
-  365000    73.852366     1000   0.67330205    5.7334066 
-  366000    74.317924     1000   0.67997811    5.7491146 
-  367000    74.781431     1000   0.67734915    5.7648225 
-  368000     75.24363     1000   0.66811078    5.7805305 
-  369000    75.704319     1000   0.67232161    5.7962384 
-  370000    76.165294     1000   0.67262944    5.8119464 
-  371000    76.624971     1000   0.68614241    5.8276544 
-  372000    77.085918     1000   0.70293842    5.8433623 
-  373000    77.544679     1000   0.71889856    5.8590703 
-  374000    78.007103     1000    0.7170296    5.8747783 
-  375000    78.468913     1000   0.71258031    5.8904862 
-  376000     78.93354     1000   0.70758873    5.9061942 
-  377000     79.39396     1000   0.69486822    5.9219022 
-  378000    79.850685     1000   0.68311194    5.9376101 
-  379000    80.307228     1000   0.67317549    5.9533181 
-  380000    80.767418     1000   0.67691049     5.969026 
-  381000    81.227579     1000   0.69231691     5.984734 
-  382000    81.686924     1000   0.69998609     6.000442 
-  383000    82.145783     1000   0.69328258    6.0161499 
-  384000    82.604827     1000   0.69903908    6.0318579 
-  385000    83.056443     1000   0.69455744    6.0475659 
-  386000    83.507131     1000   0.68865933    6.0632738 
-  387000     83.95695     1000   0.68630439    6.0789818 
-  388000    84.404079     1000    0.6800564    6.0946897 
-  389000    84.851053     1000   0.66747339    6.1103977 
-  390000    85.298614     1000   0.65695883    6.1261057 
-  391000    85.744507     1000   0.65659359    6.1418136 
-  392000    86.191348     1000   0.65933663    6.1575216 
-  393000    86.632782     1000   0.65170236    6.1732296 
-  394000    87.074105     1000   0.65631817    6.1889375 
-  395000      87.5177     1000   0.66205838    6.2046455 
-  396000    87.963111     1000   0.65512694    6.2203535 
-  397000    88.408348     1000   0.65266011    6.2360614 
-  398000    88.854042     1000   0.64593806    6.2517694 
-  399000    89.298754     1000   0.64940473    6.2674773 
-  400000    89.745445     1000   0.66033435    6.2831853 
-Loop time of 89.7455 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 9098.023 tau/day, 2228.525 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 10.924     | 10.924     | 10.924     |   0.0 | 12.17
-Neigh   | 0.10266    | 0.10266    | 0.10266    |   0.0 |  0.11
-Comm    | 1.9424     | 1.9424     | 1.9424     |   0.0 |  2.16
-Output  | 0.0056458  | 0.0056458  | 0.0056458  |   0.0 |  0.01
-Modify  | 75.442     | 75.442     | 75.442     |   0.0 | 84.06
-Other   |            | 1.329      |            |       |  1.48
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    272 ave 272 max 272 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    4933 ave 4933 max 4933 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4933
-Ave neighs/atom = 4.933
-Neighbor list builds = 171
-Dangerous builds = 0
-Total wall time: 0:02:24

examples/granregion/log.27Nov18.granregion.mixer.g++.4

@@ -1,602 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-variable	name string mixer
-
-thermo_modify	flush yes
-variable	seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable	rlo equal 0.3
-variable	rhi equal 0.6
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.3
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.6
-variable 	skin equal ${rhi}
-variable 	skin equal 0.6
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	kn equal 10^5
-variable	kt equal 0.2*${kn}
-variable	kt equal 0.2*100000
-
-variable	gravity equal 1.0
-variable	density equal 1.0
-
-variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable	a equal (-2.0*log(${coeffRes})/PI)^2
-variable	a equal (-2.0*log(0.1)/PI)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 806.699778405191*0.5
-
-variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable	dt equal ${tcol}*0.02
-variable	dt equal 0.00236257621510454*0.02
-timestep	${dt}
-timestep	4.72515243020908e-05
-
-###############################################
-
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		on
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block 0 20 0 20 0 20
-create_box	1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
-  1 by 2 by 2 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} bin
-neighbor        0.6 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0
-  ghost atom cutoff = 0
-  binsize = 20, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region	     	insreg cylinder z 10 10 8 10 18 side in units box
-region	    	cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable	theta equal (step/400000)*2*PI
-
-region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
-region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
-
-region		mixer intersect 3 cylreg b1 b2 side in
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
-thermo_modify	flush yes lost warn
-
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes
-Step CPU Atoms KinEng v_theta 
-       0            0        0           -0            0 
-    1000  0.096722603      444           -0  0.015707963 
-    2000   0.18796778      444           -0  0.031415927 
-    3000   0.27916241      444           -0   0.04712389 
-    4000   0.37111688      444           -0  0.062831853 
-    5000   0.46224833      444           -0  0.078539816 
-    6000   0.55190682      444           -0   0.09424778 
-    7000   0.64120579      444           -0   0.10995574 
-    8000   0.73025131      444           -0   0.12566371 
-    9000   0.82121348      444           -0   0.14137167 
-   10000   0.91006637      444           -0   0.15707963 
-   11000   0.97034311      444           -0    0.1727876 
-   12000     1.030247      444           -0   0.18849556 
-   13000    1.0894752      444           -0   0.20420352 
-   14000    1.1483686      444           -0   0.21991149 
-   15000    1.2138393      444           -0   0.23561945 
-   16000    1.2744856      444           -0   0.25132741 
-   17000    1.3361425      444           -0   0.26703538 
-   18000    1.3998857      444           -0   0.28274334 
-   19000    1.4625463      444           -0    0.2984513 
-   20000    1.5255082      444           -0   0.31415927 
-   21000    1.5845048      444           -0   0.32986723 
-   22000    1.6437175      444           -0   0.34557519 
-   23000    1.7022173      444           -0   0.36128316 
-   24000    1.7614172      444           -0   0.37699112 
-   25000    1.8209105      444           -0   0.39269908 
-   26000    1.8818901      444           -0   0.40840704 
-   27000    1.9439991      444           -0   0.42411501 
-   28000    2.0067189      444           -0   0.43982297 
-   29000    2.0697014      444           -0   0.45553093 
-   30000    2.1327429      444           -0    0.4712389 
-   31000    2.1904151      444           -0   0.48694686 
-   32000    2.2478669      444           -0   0.50265482 
-   33000    2.3062997      444           -0   0.51836279 
-   34000    2.3723967      444           -0   0.53407075 
-   35000    2.4331915      444           -0   0.54977871 
-   36000    2.4937904      444           -0   0.56548668 
-   37000    2.5550685      444           -0   0.58119464 
-   38000    2.6170652      444           -0    0.5969026 
-   39000    2.6789875      444           -0   0.61261057 
-   40000    2.7414019      444           -0   0.62831853 
-   41000     2.799027      444           -0   0.64402649 
-   42000    2.8570235      444           -0   0.65973446 
-   43000    2.9140713      444           -0   0.67544242 
-   44000    2.9702985      444           -0   0.69115038 
-   45000    3.0274565      444           -0   0.70685835 
-   46000    3.0860338      444           -0   0.72256631 
-   47000    3.1450455      444           -0   0.73827427 
-   48000    3.2057948      444           -0   0.75398224 
-   49000     3.267339      444           -0    0.7696902 
-   50000    3.3300545      444           -0   0.78539816 
-   51000    3.3942592      444           -0   0.80110613 
-   52000    3.4522727      444           -0   0.81681409 
-   53000    3.5117693      444           -0   0.83252205 
-   54000    3.5717957      444           -0   0.84823002 
-   55000    3.6338761      444           -0   0.86393798 
-   56000    3.7006576      444           -0   0.87964594 
-   57000    3.7648654      444           -0   0.89535391 
-   58000     3.829128      444           -0   0.91106187 
-   59000    3.8930187      444           -0   0.92676983 
-   60000    3.9581499      444           -0    0.9424778 
-   61000    4.0213017      444           -0   0.95818576 
-   62000    4.0822632      444           -0   0.97389372 
-   63000    4.1443422      444           -0   0.98960169 
-   64000    4.2072315      444           -0    1.0053096 
-   65000    4.2711387      444           -0    1.0210176 
-   66000    4.3361402      444           -0    1.0367256 
-   67000    4.4031398      444           -0    1.0524335 
-   68000    4.4698064      444           -0    1.0681415 
-   69000    4.5374978      444           -0    1.0838495 
-   70000    4.6051283      444           -0    1.0995574 
-   71000    4.6694169      444           -0    1.1152654 
-   72000    4.7335079      444           -0    1.1309734 
-   73000    4.7967482      444           -0    1.1466813 
-   74000    4.8603547      444           -0    1.1623893 
-   75000    4.9250085      444           -0    1.1780972 
-   76000    4.9909372      444           -0    1.1938052 
-   77000    5.0578024      444           -0    1.2095132 
-   78000    5.1250138      444           -0    1.2252211 
-   79000    5.1929755      444           -0    1.2409291 
-   80000    5.2627637      444           -0    1.2566371 
-   81000    5.3280981      444           -0     1.272345 
-   82000    5.3957336      444           -0     1.288053 
-   83000    5.4648135      444           -0     1.303761 
-   84000    5.5368683      444           -0    1.3194689 
-   85000    5.6352935      888           -0    1.3351769 
-   86000    5.7708502      888           -0    1.3508848 
-   87000    5.9051492      888           -0    1.3665928 
-   88000    6.0384896      888           -0    1.3823008 
-   89000    6.1714747      888           -0    1.3980087 
-   90000    6.3042989      888           -0    1.4137167 
-   91000    6.4114611      888           -0    1.4294247 
-   92000    6.5164247      888           -0    1.4451326 
-   93000    6.6219602      888           -0    1.4608406 
-   94000     6.728405      888           -0    1.4765485 
-   95000    6.8411646      888           -0    1.4922565 
-   96000    6.9479821      888           -0    1.5079645 
-   97000    7.0569239      888           -0    1.5236724 
-   98000    7.1673372      888           -0    1.5393804 
-   99000    7.2778809      888           -0    1.5550884 
-  100000     7.398834      888           -0    1.5707963 
-  101000    7.5066864      888           -0    1.5865043 
-  102000    7.6158357      888           -0    1.6022123 
-  103000     7.725111      888           -0    1.6179202 
-  104000    7.8344197      888           -0    1.6336282 
-  105000    7.9532022      888           -0    1.6493361 
-  106000    8.0643187      888           -0    1.6650441 
-  107000    8.1765473      888           -0    1.6807521 
-  108000    8.2890661      888           -0      1.69646 
-  109000    8.4048562      888           -0     1.712168 
-  110000    8.5208168      888           -0     1.727876 
-  111000    8.6303153      888           -0    1.7435839 
-  112000    8.7401052      888           -0    1.7592919 
-  113000    8.8518219      888           -0    1.7749998 
-  114000    8.9638157      888           -0    1.7907078 
-  115000    9.0766122      888           -0    1.8064158 
-  116000    9.1908746      888           -0    1.8221237 
-  117000     9.306145      888           -0    1.8378317 
-  118000    9.4229569      888           -0    1.8535397 
-  119000    9.5407412      888           -0    1.8692476 
-  120000    9.6574531      888           -0    1.8849556 
-  121000    9.7683234      888           -0    1.9006636 
-  122000    9.8812008      888           -0    1.9163715 
-  123000    9.9952521      888           -0    1.9320795 
-  124000    10.111879      888           -0    1.9477874 
-  125000    10.228812      888           -0    1.9634954 
-  126000    10.347842      888           -0    1.9792034 
-  127000     10.47052      888           -0    1.9949113 
-  128000    10.593136      888           -0    2.0106193 
-  129000    10.718124      888           -0    2.0263273 
-  130000    10.844211      888           -0    2.0420352 
-  131000    10.959177      888           -0    2.0577432 
-  132000    11.075781      888           -0    2.0734512 
-  133000    11.191418      888           -0    2.0891591 
-  134000    11.313376      888           -0    2.1048671 
-  135000    11.432321      888           -0     2.120575 
-  136000    11.551893      888           -0     2.136283 
-  137000    11.672695      888           -0     2.151991 
-  138000    11.793487      888           -0    2.1676989 
-  139000    11.914089      888           -0    2.1834069 
-  140000    12.037441      888           -0    2.1991149 
-  141000    12.161974      888           -0    2.2148228 
-  142000    12.286641      888           -0    2.2305308 
-  143000    12.414012      888           -0    2.2462387 
-  144000    12.540939      888           -0    2.2619467 
-  145000     12.66985      888           -0    2.2776547 
-  146000     12.79975      888           -0    2.2933626 
-  147000    12.932702      888           -0    2.3090706 
-  148000    13.066088      888           -0    2.3247786 
-  149000    13.200814      888           -0    2.3404865 
-  150000     13.33565      888           -0    2.3561945 
-  151000    13.465995      888           -0    2.3719025 
-  152000    13.586622      888           -0    2.3876104 
-  153000    13.711423      888           -0    2.4033184 
-  154000    13.835058      888           -0    2.4190263 
-  155000    13.967661      888           -0    2.4347343 
-  156000    14.100609      888           -0    2.4504423 
-  157000    14.234485      888           -0    2.4661502 
-  158000    14.373325      888           -0    2.4818582 
-  159000    14.510608      888           -0    2.4975662 
-  160000    14.651416      888           -0    2.5132741 
-  161000    14.785767      888           -0    2.5289821 
-  162000    14.921569      888           -0      2.54469 
-  163000    15.058895      888           -0     2.560398 
-  164000    15.198786      888           -0     2.576106 
-  165000    15.341662      888           -0    2.5918139 
-  166000    15.487128      888           -0    2.6075219 
-  167000    15.649383      888           -0    2.6232299 
-  168000    15.795388      888           -0    2.6389378 
-  169000    15.942671      888           -0    2.6546458 
-  170000    16.091824     1000           -0    2.6703538 
-  171000    16.239863     1000           -0    2.6860617 
-  172000    16.391118     1000           -0    2.7017697 
-  173000      16.5417     1000           -0    2.7174776 
-  174000     16.69479     1000           -0    2.7331856 
-  175000    16.847412     1000           -0    2.7488936 
-  176000    17.000374     1000           -0    2.7646015 
-  177000     17.15471     1000           -0    2.7803095 
-  178000     17.31284     1000           -0    2.7960175 
-  179000     17.46991     1000           -0    2.8117254 
-  180000    17.629018     1000           -0    2.8274334 
-  181000    17.787736     1000           -0    2.8431414 
-  182000    17.946197     1000           -0    2.8588493 
-  183000    18.105271     1000           -0    2.8745573 
-  184000    18.263731     1000           -0    2.8902652 
-  185000    18.433277     1000           -0    2.9059732 
-  186000    18.594456     1000           -0    2.9216812 
-  187000    18.755532     1000           -0    2.9373891 
-  188000    18.918447     1000           -0    2.9530971 
-  189000    19.080359     1000           -0    2.9688051 
-  190000    19.243927     1000           -0     2.984513 
-  191000    19.395044     1000           -0     3.000221 
-  192000    19.546837     1000           -0    3.0159289 
-  193000    19.695827     1000           -0    3.0316369 
-  194000    19.843856     1000           -0    3.0473449 
-  195000    19.993821     1000           -0    3.0630528 
-  196000    20.145787     1000           -0    3.0787608 
-  197000    20.298114     1000           -0    3.0944688 
-  198000     20.45074     1000           -0    3.1101767 
-  199000    20.607595     1000           -0    3.1258847 
-  200000    20.760979     1000           -0    3.1415927 
-Loop time of 20.7611 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 39328.699 tau/day, 9633.409 timesteps/s
-98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.57172    | 0.93292    | 1.2995     |  37.1 |  4.49
-Neigh   | 0.015648   | 0.018747   | 0.02175    |   2.1 |  0.09
-Comm    | 3.17       | 3.6151     | 4.0856     |  23.0 | 17.41
-Output  | 0.0051017  | 0.012686   | 0.033359   |  10.6 |  0.06
-Modify  | 12.36      | 13.269     | 14.095     |  21.8 | 63.91
-Other   |            | 2.912      |            |       | 14.03
-
-Nlocal:    250 ave 270 max 230 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost:    297 ave 337 max 234 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    982.5 ave 1580 max 496 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 3930
-Ave neighs/atom = 3.93
-Neighbor list builds = 218
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 12 | 12.19 | 12.35 Mbytes
-Step CPU Atoms KinEng v_theta 
-  200000            0     1000   0.89289812    3.1415927 
-  201000   0.15554476     1000   0.90162438    3.1573006 
-  202000   0.31118774     1000   0.89175077    3.1730086 
-  203000   0.47266722     1000   0.88068523    3.1887165 
-  204000   0.64758801     1000   0.88775074    3.2044245 
-  205000   0.85137105     1000   0.89009449    3.2201325 
-  206000    1.0712745     1000   0.89031724    3.2358404 
-  207000    1.3620427     1000   0.90901476    3.2515484 
-  208000    1.6051998     1000   0.91977358    3.2672564 
-  209000    1.7975032     1000   0.92044257    3.2829643 
-  210000    1.9654117     1000   0.90550844    3.2986723 
-  211000    2.1186137     1000   0.90179135    3.3143802 
-  212000    2.2714169     1000   0.90474936    3.3300882 
-  213000    2.4236252     1000    0.9011002    3.3457962 
-  214000    2.5737655     1000   0.89619815    3.3615041 
-  215000    2.7326233     1000   0.89129064    3.3772121 
-  216000    2.8794787     1000   0.88785486    3.3929201 
-  217000    3.0264313     1000   0.89448821     3.408628 
-  218000    3.1743443     1000   0.89323746     3.424336 
-  219000    3.3225086     1000   0.88176869     3.440044 
-  220000    3.4717121     1000   0.86989815    3.4557519 
-  221000    3.6229391     1000   0.85900389    3.4714599 
-  222000    3.7768724     1000   0.85440461    3.4871678 
-  223000    3.9287963     1000    0.8604449    3.5028758 
-  224000     4.082505     1000   0.84537374    3.5185838 
-  225000     4.234731     1000   0.84526488    3.5342917 
-  226000    4.3872988     1000   0.85877362    3.5499997 
-  227000    4.5396216     1000   0.86762074    3.5657077 
-  228000    4.7092509     1000   0.86460359    3.5814156 
-  229000    4.8631954     1000   0.85409682    3.5971236 
-  230000    5.0194352     1000   0.83902718    3.6128316 
-  231000    5.1765387     1000   0.83908755    3.6285395 
-  232000    5.3335299     1000   0.83178808    3.6442475 
-  233000    5.4917257     1000   0.83369584    3.6599554 
-  234000     5.654233     1000    0.8530074    3.6756634 
-  235000    5.8163757     1000   0.86385009    3.6913714 
-  236000    5.9791231     1000   0.86453337    3.7070793 
-  237000    6.1401029     1000   0.86137572    3.7227873 
-  238000     6.300632     1000    0.8656285    3.7384953 
-  239000    6.4597898     1000   0.85993724    3.7542032 
-  240000    6.6216707     1000    0.8484153    3.7699112 
-  241000    6.7793672     1000   0.84624799    3.7856191 
-  242000     6.939244     1000   0.83739227    3.8013271 
-  243000    7.1013088     1000   0.83026469    3.8170351 
-  244000     7.267416     1000   0.81060567     3.832743 
-  245000    7.4318523     1000   0.81081038     3.848451 
-  246000    7.6077905     1000   0.80857771     3.864159 
-  247000    7.7763391     1000   0.80353315    3.8798669 
-  248000    7.9485247     1000   0.80191903    3.8955749 
-  249000    8.1208956     1000   0.79865102    3.9112829 
-  250000    8.2921841     1000   0.79407385    3.9269908 
-  251000    8.4614651     1000    0.7880275    3.9426988 
-  252000    8.6266186     1000   0.79212521    3.9584067 
-  253000    8.7913449     1000   0.78976714    3.9741147 
-  254000    8.9596558     1000   0.79720779    3.9898227 
-  255000    9.1278918     1000   0.79329363    4.0055306 
-  256000    9.3016815     1000   0.80851295    4.0212386 
-  257000    9.4701304     1000   0.82322071    4.0369466 
-  258000    9.6399531     1000   0.83042211    4.0526545 
-  259000    9.8090186     1000   0.82773068    4.0683625 
-  260000    9.9798045     1000    0.8246773    4.0840704 
-  261000    10.148952     1000   0.81374287    4.0997784 
-  262000    10.318855     1000   0.79936963    4.1154864 
-  263000    10.496092     1000   0.78124408    4.1311943 
-  264000    10.671031     1000   0.77790646    4.1469023 
-  265000    10.843052     1000   0.77212005    4.1626103 
-  266000     11.01867     1000   0.77977752    4.1783182 
-  267000    11.192151     1000   0.79237542    4.1940262 
-  268000    11.362491     1000   0.80631398    4.2097342 
-  269000     11.53223     1000   0.82380407    4.2254421 
-  270000      11.7123     1000   0.82477127    4.2411501 
-  271000    11.883593     1000   0.81655074     4.256858 
-  272000    12.052348     1000   0.80678676     4.272566 
-  273000    12.220196     1000   0.79162789     4.288274 
-  274000    12.395164     1000   0.78896081    4.3039819 
-  275000    12.569757     1000   0.77904648    4.3196899 
-  276000    12.748754     1000   0.78252999    4.3353979 
-  277000     12.91648     1000   0.78293295    4.3511058 
-  278000    13.086087     1000   0.78311337    4.3668138 
-  279000    13.260159     1000   0.77657634    4.3825218 
-  280000    13.428503     1000   0.76835711    4.3982297 
-  281000    13.596094     1000   0.75586438    4.4139377 
-  282000    13.763325     1000   0.74600306    4.4296456 
-  283000    13.932867     1000   0.73228762    4.4453536 
-  284000    14.098865     1000   0.72344939    4.4610616 
-  285000    14.269317     1000   0.72160289    4.4767695 
-  286000    14.441196     1000   0.71321619    4.4924775 
-  287000    14.614458     1000   0.72631772    4.5081855 
-  288000    14.783358     1000   0.74390396    4.5238934 
-  289000    14.953564     1000   0.77320352    4.5396014 
-  290000     15.12428     1000   0.77249469    4.5553093 
-  291000    15.283974     1000    0.7583723    4.5710173 
-  292000    15.449553     1000   0.74568347    4.5867253 
-  293000    15.611965     1000   0.74108034    4.6024332 
-  294000    15.770807     1000   0.72706174    4.6181412 
-  295000    15.927151     1000   0.71122597    4.6338492 
-  296000    16.086734     1000   0.70272297    4.6495571 
-  297000    16.245418     1000    0.6945394    4.6652651 
-  298000    16.406617     1000   0.69541258    4.6809731 
-  299000    16.568989     1000   0.71696092     4.696681 
-  300000    16.754911     1000   0.72939561     4.712389 
-  301000    16.919453     1000   0.73621801    4.7280969 
-  302000     17.07794     1000   0.72052605    4.7438049 
-  303000    17.234397     1000   0.71057318    4.7595129 
-  304000     17.39014     1000   0.70014814    4.7752208 
-  305000    17.550789     1000   0.68855925    4.7909288 
-  306000    17.718802     1000   0.68665019    4.8066368 
-  307000    17.874036     1000    0.6831349    4.8223447 
-  308000    18.029367     1000   0.67929468    4.8380527 
-  309000    18.188065     1000   0.67833006    4.8537606 
-  310000    18.348243     1000   0.67764037    4.8694686 
-  311000    18.512475     1000   0.68271978    4.8851766 
-  312000    18.676519     1000   0.69021026    4.9008845 
-  313000    18.836426     1000   0.68795473    4.9165925 
-  314000    18.997681     1000   0.68308892    4.9323005 
-  315000    19.158794     1000   0.68086977    4.9480084 
-  316000    19.318186     1000   0.67879169    4.9637164 
-  317000    19.479364     1000   0.68128526    4.9794244 
-  318000    19.645085     1000   0.68718719    4.9951323 
-  319000    19.806831     1000   0.68419901    5.0108403 
-  320000     19.97005     1000   0.68045269    5.0265482 
-  321000    20.130643     1000   0.68430036    5.0422562 
-  322000    20.291637     1000   0.68195368    5.0579642 
-  323000    20.457605     1000   0.67964011    5.0736721 
-  324000    20.621699     1000   0.67681293    5.0893801 
-  325000     20.78525     1000   0.67601868    5.1050881 
-  326000    20.950321     1000   0.67600265     5.120796 
-  327000     21.11346     1000   0.68484094     5.136504 
-  328000    21.276964     1000   0.68526189     5.152212 
-  329000    21.440971     1000   0.67602072    5.1679199 
-  330000    21.609791     1000   0.68222852    5.1836279 
-  331000    21.773574     1000   0.68825647    5.1993358 
-  332000     21.93854     1000   0.68168415    5.2150438 
-  333000    22.102281     1000   0.67460357    5.2307518 
-  334000    22.265741     1000   0.67747925    5.2464597 
-  335000    22.436954     1000     0.681763    5.2621677 
-  336000    22.614367     1000   0.67611867    5.2778757 
-  337000    22.779064     1000   0.66903217    5.2935836 
-  338000    22.945739     1000    0.6684293    5.3092916 
-  339000    23.111375     1000   0.66465194    5.3249995 
-  340000    23.278674     1000   0.66226848    5.3407075 
-  341000    23.444642     1000   0.66407188    5.3564155 
-  342000    23.614615     1000   0.65762812    5.3721234 
-  343000    23.785007     1000   0.66936507    5.3878314 
-  344000    23.956265     1000   0.67424224    5.4035394 
-  345000    24.129057     1000     0.684271    5.4192473 
-  346000    24.303073     1000   0.68294352    5.4349553 
-  347000    24.475812     1000   0.69795697    5.4506633 
-  348000    24.652771     1000   0.69818863    5.4663712 
-  349000    24.830973     1000   0.69578798    5.4820792 
-  350000     25.00923     1000   0.69377251    5.4977871 
-  351000    25.185421     1000   0.69638202    5.5134951 
-  352000    25.363647     1000   0.70115823    5.5292031 
-  353000    25.540517     1000   0.70891635     5.544911 
-  354000    25.718709     1000   0.70876639     5.560619 
-  355000    25.893633     1000   0.71130235     5.576327 
-  356000    26.068423     1000   0.69380913    5.5920349 
-  357000    26.243801     1000   0.67934899    5.6077429 
-  358000    26.418883     1000   0.67024516    5.6234508 
-  359000    26.594722     1000   0.66145645    5.6391588 
-  360000    26.770322     1000   0.65335546    5.6548668 
-  361000    26.946396     1000   0.65495192    5.6705747 
-  362000     27.12296     1000   0.64973833    5.6862827 
-  363000    27.298461     1000   0.64532381    5.7019907 
-  364000    27.473586     1000   0.64282855    5.7176986 
-  365000    27.653872     1000   0.64451862    5.7334066 
-  366000    27.830317     1000   0.64366439    5.7491146 
-  367000    28.007037     1000   0.64395479    5.7648225 
-  368000    28.184079     1000   0.65827587    5.7805305 
-  369000    28.376009     1000   0.66311341    5.7962384 
-  370000    28.557287     1000   0.66165026    5.8119464 
-  371000    28.736569     1000   0.66878374    5.8276544 
-  372000     28.91063     1000   0.66944548    5.8433623 
-  373000    29.084648     1000   0.66061945    5.8590703 
-  374000    29.258649     1000   0.65320954    5.8747783 
-  375000    29.433156     1000   0.64641195    5.8904862 
-  376000    29.611781     1000   0.64631388    5.9061942 
-  377000     29.78531     1000   0.64232398    5.9219022 
-  378000    29.955917     1000   0.63805257    5.9376101 
-  379000    30.126378     1000   0.63666047    5.9533181 
-  380000    30.297285     1000   0.63651856     5.969026 
-  381000    30.471635     1000    0.6377374     5.984734 
-  382000    30.644813     1000   0.64750107     6.000442 
-  383000    30.816208     1000   0.65655138    6.0161499 
-  384000    30.986444     1000   0.65408935    6.0318579 
-  385000    31.156501     1000   0.64437236    6.0475659 
-  386000    31.327665     1000   0.63862174    6.0632738 
-  387000     31.49731     1000   0.64133807    6.0789818 
-  388000    31.682031     1000   0.64174374    6.0946897 
-  389000     31.85148     1000   0.64480071    6.1103977 
-  390000    32.020336     1000   0.64982943    6.1261057 
-  391000    32.187634     1000    0.6461109    6.1418136 
-  392000    32.357282     1000   0.64044412    6.1575216 
-  393000    32.527796     1000   0.64662995    6.1732296 
-  394000    32.704323     1000   0.65330527    6.1889375 
-  395000    32.880643     1000   0.66026265    6.2046455 
-  396000    33.048614     1000    0.6718969    6.2203535 
-  397000    33.222059     1000   0.66481385    6.2360614 
-  398000    33.391738     1000   0.66685494    6.2517694 
-  399000    33.560431     1000    0.6612594    6.2674773 
-  400000    33.729715     1000   0.65289572    6.2831853 
-Loop time of 33.7298 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 24207.249 tau/day, 5929.470 timesteps/s
-97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.6748     | 2.6848     | 3.6646     |  58.4 |  7.96
-Neigh   | 0.021206   | 0.026438   | 0.03191    |   3.1 |  0.08
-Comm    | 6.133      | 7.3745     | 8.6652     |  45.0 | 21.86
-Output  | 0.0053763  | 0.016101   | 0.044719   |  13.0 |  0.05
-Modify  | 18.26      | 20.115     | 22.413     |  39.2 | 59.64
-Other   |            | 3.513      |            |       | 10.42
-
-Nlocal:    250 ave 266 max 230 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Nghost:    401.5 ave 476 max 325 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    1264 ave 1634 max 895 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 5056
-Ave neighs/atom = 5.056
-Neighbor list builds = 160
-Dangerous builds = 0
-Total wall time: 0:00:54

examples/granular/in.pour.drum

@@ -44,7 +44,7 @@ change_box      all boundary p p f
 
 pair_style      granular
 pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall 
 
 variable        theta equal 0
 

examples/granular/in.pour.heat

@@ -0,0 +1,84 @@
+# pour one types of particles into cylinder and oscillate
+# temperature of the bottom plate
+
+variable        name string heat_plate
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 10
+variable        boxy equal 10
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_height equal 30
+
+variable        xc equal 0.5*${boxx}
+variable        yc equal 0.5*${boxx}
+variable        zc equal 0.5*${boxz}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dhi equal 2.0*${rhi}
+
+variable        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box      2 boxreg
+change_box      all boundary p p f
+
+pair_style      granular
+pair_coeff      * * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+
+fix             0 all property/atom temperature heatflow
+fix             1 all balance 100 1.0 shift xy 5 1.1
+fix             2 all nve/sphere
+fix             3 all heat/flow constant 1.0
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 1000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify     vel yes
+
+neighbor        ${skin} bin
+neigh_modify    delay 0 every 1 check yes
+
+variable        oscillate equal 1.0*sin(step*0.0001)
+
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0 region bottom_wall temperature v_oscillate
+
+thermo_style    custom step atoms ke pxx pyy pzz
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 1000 ${name}.dump id type radius mass x y z temperature heatflow
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+group           delgroup dynamic all var zmax every 10000
+
+run             100000
+

examples/granular/log.15Sep22.pour.drum.g++.1

@@ -0,0 +1,272 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable        name string rotating_drum_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 30
+variable        boxy equal 30
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_rad equal 30*0.5
+variable        drum_height equal 20
+
+variable        xc equal 0.5*${boxx}
+variable        xc equal 0.5*30
+variable        yc equal 0.5*${boxx}
+variable        yc equal 0.5*30
+variable        zc equal 0.5*${boxz}
+variable        zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 30 0 ${boxz}
+region          boxreg block 0 30 0 30 0 50
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  1 by 1 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
+
+variable        theta equal 0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 20 ${boxz}
+region          insreg cylinder z 15 15 14.45 20 50
+
+fix             0 all balance 100 1.0 shift xy 5 1.1
+fix             1 all nve/sphere
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix             ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify     vel yes
+
+neighbor        ${skin} bin
+neighbor        0.2 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style    custom step atoms ke v_theta
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+variable        zmax atom z+c_1>0.5*20
+group           delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run             2000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes
+   Step        Atoms        KinEng        v_theta    
+         0           0  -0              0            
+       100        4000  -0              0            
+       200        4000  -0              0            
+       300        4000  -0              0            
+       400        4000  -0              0            
+       500        4000  -0              0            
+       600        4000  -0              0            
+       700        4000  -0              0            
+       800        4000  -0              0            
+       900        4000  -0              0            
+      1000        4000  -0              0            
+      1100        4000  -0              0            
+      1200        4000  -0              0            
+      1300        4000  -0              0            
+      1400        4000  -0              0            
+      1500        4000  -0              0            
+      1600        4000  -0              0            
+      1700        4000  -0              0            
+      1800        4000  -0              0            
+      1900        4000  -0              0            
+      2000        4000  -0              0            
+Loop time of 2.81549 on 1 procs for 2000 steps with 4000 atoms
+
+Performance: 61374.657 tau/day, 710.355 timesteps/s, 2.841 Matom-step/s
+98.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.35362    | 0.35362    | 0.35362    |   0.0 | 12.56
+Neigh   | 1.0852     | 1.0852     | 1.0852     |   0.0 | 38.54
+Comm    | 0.041891   | 0.041891   | 0.041891   |   0.0 |  1.49
+Output  | 0.00059151 | 0.00059151 | 0.00059151 |   0.0 |  0.02
+Modify  | 1.2814     | 1.2814     | 1.2814     |   0.0 | 45.51
+Other   |            | 0.0528     |            |       |  1.88
+
+Nlocal:           4000 ave        4000 max        4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            179 ave         179 max         179 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           7019 ave        7019 max        7019 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7019
+Ave neighs/atom = 1.75475
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms    group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region          top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix           grav
+unfix           ins1
+unfix           ins2
+fix             grav all gravity 10 vector 0 -1 0
+
+variable        theta equal 2*PI*elapsed/20000.0
+run             3000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 22.42 | 22.42 | 22.42 Mbytes
+   Step        Atoms        KinEng        v_theta    
+      2000        4000   59.969827      0            
+      2100        4000   47.251389      0.031415927  
+      2200        4000   33.726755      0.062831853  
+      2300        4000   24.212479      0.09424778   
+      2400        4000   17.366268      0.12566371   
+      2500        4000   18.502318      0.15707963   
+      2600        4000   17.44981       0.18849556   
+      2700        4000   16.068315      0.21991149   
+      2800        4000   14.252644      0.25132741   
+      2900        4000   11.544019      0.28274334   
+      3000        4000   9.0353662      0.31415927   
+      3100        4000   6.9955912      0.34557519   
+      3200        4000   5.955137       0.37699112   
+      3300        4000   5.8947849      0.40840704   
+      3400        4000   6.0544729      0.43982297   
+      3500        4000   6.5326359      0.4712389    
+      3600        4000   6.6047764      0.50265482   
+      3700        4000   6.7073614      0.53407075   
+      3800        4000   6.7367804      0.56548668   
+      3900        4000   6.6178006      0.5969026    
+      4000        4000   6.3834858      0.62831853   
+      4100        4000   5.8660652      0.65973446   
+      4200        4000   5.308513       0.69115038   
+      4300        4000   4.7270842      0.72256631   
+      4400        4000   4.1920733      0.75398224   
+      4500        4000   3.7068814      0.78539816   
+      4600        4000   3.3259615      0.81681409   
+      4700        4000   2.9339231      0.84823002   
+      4800        4000   2.670752       0.87964594   
+      4900        4000   2.4509115      0.91106187   
+      5000        4000   2.2609335      0.9424778    
+Loop time of 9.82178 on 1 procs for 3000 steps with 4000 atoms
+
+Performance: 26390.330 tau/day, 305.444 timesteps/s, 1.222 Matom-step/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.2932     | 3.2932     | 3.2932     |   0.0 | 33.53
+Neigh   | 2.2872     | 2.2872     | 2.2872     |   0.0 | 23.29
+Comm    | 0.067117   | 0.067117   | 0.067117   |   0.0 |  0.68
+Output  | 0.00093425 | 0.00093425 | 0.00093425 |   0.0 |  0.01
+Modify  | 4.0986     | 4.0986     | 4.0986     |   0.0 | 41.73
+Other   |            | 0.07476    |            |       |  0.76
+
+Nlocal:           4000 ave        4000 max        4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            363 ave         363 max         363 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13089 ave       13089 max       13089 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13089
+Ave neighs/atom = 3.27225
+Neighbor list builds = 1247
+Dangerous builds = 130
+Total wall time: 0:00:12

examples/granular/log.15Sep22.pour.drum.g++.4

@@ -0,0 +1,272 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable        name string rotating_drum_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 30
+variable        boxy equal 30
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_rad equal 30*0.5
+variable        drum_height equal 20
+
+variable        xc equal 0.5*${boxx}
+variable        xc equal 0.5*30
+variable        yc equal 0.5*${boxx}
+variable        yc equal 0.5*30
+variable        zc equal 0.5*${boxz}
+variable        zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 30 0 ${boxz}
+region          boxreg block 0 30 0 30 0 50
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  2 by 2 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
+
+variable        theta equal 0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 20 ${boxz}
+region          insreg cylinder z 15 15 14.45 20 50
+
+fix             0 all balance 100 1.0 shift xy 5 1.1
+fix             1 all nve/sphere
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix             ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify     vel yes
+
+neighbor        ${skin} bin
+neighbor        0.2 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style    custom step atoms ke v_theta
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+variable        zmax atom z+c_1>0.5*20
+group           delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run             2000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.3 | 15.3 | 15.3 Mbytes
+   Step        Atoms        KinEng        v_theta    
+         0           0  -0              0            
+       100        4000  -0              0            
+       200        4000  -0              0            
+       300        4000  -0              0            
+       400        4000  -0              0            
+       500        4000  -0              0            
+       600        4000  -0              0            
+       700        4000  -0              0            
+       800        4000  -0              0            
+       900        4000  -0              0            
+      1000        4000  -0              0            
+      1100        4000  -0              0            
+      1200        4000  -0              0            
+      1300        4000  -0              0            
+      1400        4000  -0              0            
+      1500        4000  -0              0            
+      1600        4000  -0              0            
+      1700        4000  -0              0            
+      1800        4000  -0              0            
+      1900        4000  -0              0            
+      2000        4000  -0              0            
+Loop time of 0.744926 on 4 procs for 2000 steps with 4000 atoms
+
+Performance: 231969.322 tau/day, 2684.830 timesteps/s, 10.739 Matom-step/s
+98.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.064917   | 0.069813   | 0.074844   |   1.7 |  9.37
+Neigh   | 0.15075    | 0.15915    | 0.1692     |   1.9 | 21.36
+Comm    | 0.11223    | 0.11821    | 0.12247    |   1.1 | 15.87
+Output  | 0.00030739 | 0.00036898 | 0.00046777 |   0.0 |  0.05
+Modify  | 0.36068    | 0.36657    | 0.37031    |   0.7 | 49.21
+Other   |            | 0.03082    |            |       |  4.14
+
+Nlocal:           1000 ave        1010 max         990 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            285 ave         287 max         283 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:        1714.25 ave        1764 max        1651 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 6857
+Ave neighs/atom = 1.71425
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms    group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region          top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix           grav
+unfix           ins1
+unfix           ins2
+fix             grav all gravity 10 vector 0 -1 0
+
+variable        theta equal 2*PI*elapsed/20000.0
+run             3000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 21.6 | 21.6 | 21.6 Mbytes
+   Step        Atoms        KinEng        v_theta    
+      2000        4000   60.10546       0            
+      2100        4000   47.274123      0.031415927  
+      2200        4000   33.475582      0.062831853  
+      2300        4000   24.083669      0.09424778   
+      2400        4000   17.36351       0.12566371   
+      2500        4000   18.576501      0.15707963   
+      2600        4000   17.39          0.18849556   
+      2700        4000   15.789254      0.21991149   
+      2800        4000   14.08156       0.25132741   
+      2900        4000   11.636681      0.28274334   
+      3000        4000   8.9897685      0.31415927   
+      3100        4000   7.0703519      0.34557519   
+      3200        4000   6.0741809      0.37699112   
+      3300        4000   5.8286097      0.40840704   
+      3400        4000   6.059001       0.43982297   
+      3500        4000   6.4310861      0.4712389    
+      3600        4000   6.3957528      0.50265482   
+      3700        4000   6.4858292      0.53407075   
+      3800        4000   6.4685962      0.56548668   
+      3900        4000   6.3469676      0.5969026    
+      4000        4000   6.2808022      0.62831853   
+      4100        4000   5.957048       0.65973446   
+      4200        4000   5.5378951      0.69115038   
+      4300        4000   4.8523264      0.72256631   
+      4400        4000   4.2485239      0.75398224   
+      4500        4000   3.7587486      0.78539816   
+      4600        4000   3.327008       0.81681409   
+      4700        4000   2.9421013      0.84823002   
+      4800        4000   2.75247        0.87964594   
+      4900        4000   2.5306332      0.91106187   
+      5000        4000   2.352504       0.9424778    
+Loop time of 2.48704 on 4 procs for 3000 steps with 4000 atoms
+
+Performance: 104220.238 tau/day, 1206.253 timesteps/s, 4.825 Matom-step/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.51605    | 0.70407    | 0.86299    |  14.7 | 28.31
+Neigh   | 0.3522     | 0.42808    | 0.50041    |   8.0 | 17.21
+Comm    | 0.17318    | 0.42324    | 0.7046     |  29.0 | 17.02
+Output  | 0.00079725 | 0.0013956  | 0.002092   |   1.3 |  0.06
+Modify  | 0.68507    | 0.79676    | 0.90954    |   8.9 | 32.04
+Other   |            | 0.1335     |            |       |  5.37
+
+Nlocal:           1000 ave        1330 max         670 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:          525.5 ave         781 max         417 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:        3243.75 ave        4460 max        2012 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 12975
+Ave neighs/atom = 3.24375
+Neighbor list builds = 1299
+Dangerous builds = 129
+Total wall time: 0:00:03

examples/granular/log.15Sep22.pour.flatwall.g++.1

@@ -0,0 +1,195 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable        name string pour_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 20
+variable        boxy equal 20
+variable        boxz equal 30
+
+variable        xc1 equal 0.3*${boxx}
+variable        xc1 equal 0.3*20
+variable        xc2 equal 0.7*${boxx}
+variable        xc2 equal 0.7*20
+variable        yc equal 0.5*${boxy}
+variable        yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors      * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 20 0 ${boxz}
+region          boxreg block 0 20 0 20 0 30
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  1 by 1 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff      2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+comm_modify     vel yes
+
+region          insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 30
+region          insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 30
+
+fix             1 all nve/sphere
+fix             grav all gravity 10.0 vector 0 0 -1
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+neighbor        ${skin} bin
+neighbor        0.15 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style    custom step atoms ke
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.27 | 15.27 | 15.27 Mbytes
+   Step        Atoms        KinEng    
+         0           0  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100         926  -0            
+       200         926  -0            
+       300         926  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       400        1498  -0            
+       500        1498  -0            
+       600        1498  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       700        2275  -0            
+       800        2275  -0            
+       900        2275  -0            
+      1000        2275  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1100        2954  -0            
+      1200        2954  -0            
+      1300        2954  -0            
+      1400        3000  -0            
+      1500        3000  -0            
+      1600        3000  -0            
+      1700        3000  -0            
+      1800        3000  -0            
+      1900        3000  -0            
+      2000        3000  -0            
+      2100        3000  -0            
+      2200        3000  -0            
+      2300        3000  -0            
+      2400        3000  -0            
+      2500        3000  -0            
+      2600        3000  -0            
+      2700        3000  -0            
+      2800        3000  -0            
+      2900        3000  -0            
+      3000        3000  -0            
+      3100        3000  -0            
+      3200        3000  -0            
+      3300        3000  -0            
+      3400        3000  -0            
+      3500        3000  -0            
+      3600        3000  -0            
+      3700        3000  -0            
+      3800        3000  -0            
+      3900        3000  -0            
+      4000        3000  -0            
+      4100        3000  -0            
+      4200        3000  -0            
+      4300        3000  -0            
+      4400        3000  -0            
+      4500        3000  -0            
+      4600        3000  -0            
+      4700        3000  -0            
+      4800        3000  -0            
+      4900        3000  -0            
+      5000        3000  -0            
+Loop time of 10.7721 on 1 procs for 5000 steps with 3000 atoms
+
+Performance: 40103.467 tau/day, 464.160 timesteps/s, 1.392 Matom-step/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.1117     | 8.1117     | 8.1117     |   0.0 | 75.30
+Neigh   | 1.2885     | 1.2885     | 1.2885     |   0.0 | 11.96
+Comm    | 0.059888   | 0.059888   | 0.059888   |   0.0 |  0.56
+Output  | 0.0011158  | 0.0011158  | 0.0011158  |   0.0 |  0.01
+Modify  | 1.2436     | 1.2436     | 1.2436     |   0.0 | 11.54
+Other   |            | 0.06727    |            |       |  0.62
+
+Nlocal:           3000 ave        3000 max        3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            471 ave         471 max         471 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          16713 ave       16713 max       16713 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 16713
+Ave neighs/atom = 5.571
+Neighbor list builds = 1102
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/granular/log.15Sep22.pour.flatwall.g++.4

@@ -0,0 +1,195 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable        name string pour_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 20
+variable        boxy equal 20
+variable        boxz equal 30
+
+variable        xc1 equal 0.3*${boxx}
+variable        xc1 equal 0.3*20
+variable        xc2 equal 0.7*${boxx}
+variable        xc2 equal 0.7*20
+variable        yc equal 0.5*${boxy}
+variable        yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors      * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 20 0 ${boxz}
+region          boxreg block 0 20 0 20 0 30
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  2 by 2 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff      2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+comm_modify     vel yes
+
+region          insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 30
+region          insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 30
+
+fix             1 all nve/sphere
+fix             grav all gravity 10.0 vector 0 0 -1
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+neighbor        ${skin} bin
+neighbor        0.15 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style    custom step atoms ke
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.04 | 15.04 | 15.04 Mbytes
+   Step        Atoms        KinEng    
+         0           0  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100         926  -0            
+       200         926  -0            
+       300         926  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       400        1498  -0            
+       500        1498  -0            
+       600        1498  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       700        2275  -0            
+       800        2275  -0            
+       900        2275  -0            
+      1000        2275  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1100        2954  -0            
+      1200        2954  -0            
+      1300        2954  -0            
+      1400        3000  -0            
+      1500        3000  -0            
+      1600        3000  -0            
+      1700        3000  -0            
+      1800        3000  -0            
+      1900        3000  -0            
+      2000        3000  -0            
+      2100        3000  -0            
+      2200        3000  -0            
+      2300        3000  -0            
+      2400        3000  -0            
+      2500        3000  -0            
+      2600        3000  -0            
+      2700        3000  -0            
+      2800        3000  -0            
+      2900        3000  -0            
+      3000        3000  -0            
+      3100        3000  -0            
+      3200        3000  -0            
+      3300        3000  -0            
+      3400        3000  -0            
+      3500        3000  -0            
+      3600        3000  -0            
+      3700        3000  -0            
+      3800        3000  -0            
+      3900        3000  -0            
+      4000        3000  -0            
+      4100        3000  -0            
+      4200        3000  -0            
+      4300        3000  -0            
+      4400        3000  -0            
+      4500        3000  -0            
+      4600        3000  -0            
+      4700        3000  -0            
+      4800        3000  -0            
+      4900        3000  -0            
+      5000        3000  -0            
+Loop time of 4.06277 on 4 procs for 5000 steps with 3000 atoms
+
+Performance: 106331.276 tau/day, 1230.686 timesteps/s, 3.692 Matom-step/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.85426    | 1.7801     | 2.7631     |  64.4 | 43.82
+Neigh   | 0.18775    | 0.25657    | 0.3279     |  11.5 |  6.32
+Comm    | 0.23605    | 1.3334     | 2.3703     |  81.6 | 32.82
+Output  | 0.00059456 | 0.0008165  | 0.0012002  |   0.0 |  0.02
+Modify  | 0.59336    | 0.64066    | 0.6864     |   4.3 | 15.77
+Other   |            | 0.05122    |            |       |  1.26
+
+Nlocal:            750 ave        1032 max         463 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:          426.5 ave         482 max         375 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:        4164.25 ave        6310 max        1941 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 16657
+Ave neighs/atom = 5.5523333
+Neighbor list builds = 1114
+Dangerous builds = 0
+Total wall time: 0:00:04

examples/granular/log.29Oct20.pour.drum.g++.1

@@ -1,271 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) into cylinder
-# 'turn' cylinder by changing direction of gravity, then rotate it.
-# This simulates a rotating drum powder characterization experiment.
-
-variable	name string rotating_drum_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 30
-variable	boxy equal 30
-variable	boxz equal 50
-
-variable	drum_rad equal ${boxx}*0.5
-variable	drum_rad equal 30*0.5
-variable	drum_height equal 20
-
-variable	xc equal 0.5*${boxx}
-variable	xc equal 0.5*30
-variable	yc equal 0.5*${boxx}
-variable	yc equal 0.5*30
-variable	zc equal 0.5*${boxz}
-variable	zc equal 0.5*50
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.4*${rhi}
-variable skin equal 0.4*0.5
-
-#############
-processors * * 1
-region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 30 0 ${boxz}
-region		boxreg block 0 30 0 30 0 50
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
-  1 by 1 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
-
-variable	theta equal 0
-
-region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
-region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
-
-region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 20 ${boxz}
-region		insreg cylinder z 15 15 14.45 20 50
-
-fix		0 all balance 100 1.0 shift xy 5 1.1
-fix		1 all nve/sphere
-fix		grav all gravity 10 vector 0 0 -1
-fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
-fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
-
-comm_modify	vel yes
-
-neighbor	${skin} bin
-neighbor	0.2 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
-fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
-
-thermo_style	custom step atoms ke v_theta
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-#For removal later
-compute		1 all property/atom radius
-variable	zmax atom z+c_1>0.5*${drum_height}
-variable	zmax atom z+c_1>0.5*20
-group		delgroup dynamic all var zmax every 10000
-dynamic group delgroup defined
-
-run		2000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 50 50 84
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair granular, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 13.03 | 13.03 | 13.03 Mbytes
-Step Atoms KinEng v_theta 
-       0        0           -0            0 
-     100     4000           -0            0 
-     200     4000           -0            0 
-     300     4000           -0            0 
-     400     4000           -0            0 
-     500     4000           -0            0 
-     600     4000           -0            0 
-     700     4000           -0            0 
-     800     4000           -0            0 
-     900     4000           -0            0 
-    1000     4000           -0            0 
-    1100     4000           -0            0 
-    1200     4000           -0            0 
-    1300     4000           -0            0 
-    1400     4000           -0            0 
-    1500     4000           -0            0 
-    1600     4000           -0            0 
-    1700     4000           -0            0 
-    1800     4000           -0            0 
-    1900     4000           -0            0 
-    2000     4000           -0            0 
-Loop time of 10.5178 on 1 procs for 2000 steps with 4000 atoms
-
-Performance: 16429.309 tau/day, 190.154 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0701     | 1.0701     | 1.0701     |   0.0 | 10.17
-Neigh   | 4.2135     | 4.2135     | 4.2135     |   0.0 | 40.06
-Comm    | 0.38276    | 0.38276    | 0.38276    |   0.0 |  3.64
-Output  | 0.0013647  | 0.0013647  | 0.0013647  |   0.0 |  0.01
-Modify  | 4.7076     | 4.7076     | 4.7076     |   0.0 | 44.76
-Other   |            | 0.1424     |            |       |  1.35
-
-Nlocal:        4000.00 ave        4000 max        4000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        171.000 ave         171 max         171 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        8093.00 ave        8093 max        8093 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 8093
-Ave neighs/atom = 2.0232500
-Neighbor list builds = 1004
-Dangerous builds = 4
-
-#Remove any particles that are above z > 0.5*drum_height
-delete_atoms	group delgroup
-Deleted 0 atoms, new total = 4000
-
-#Add top lid
-region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
-fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
-
-# 'Turn' drum by switching the direction of gravity
-unfix		grav
-unfix		ins1
-unfix		ins2
-fix		grav all gravity 10 vector 0 -1 0
-
-variable	theta equal 2*PI*elapsed/20000.0
-run		3000
-Per MPI rank memory allocation (min/avg/max) = 19.37 | 19.37 | 19.37 Mbytes
-Step Atoms KinEng v_theta 
-    2000     4000    65.647582            0 
-    2100     4000    105.60001  0.031415927 
-    2200     4000    112.27573  0.062831853 
-    2300     4000    92.758671   0.09424778 
-    2400     4000    88.925835   0.12566371 
-    2500     4000    81.369163   0.15707963 
-    2600     4000    32.046943   0.18849556 
-    2700     4000    4.1926368   0.21991149 
-    2800     4000    3.9933453   0.25132741 
-    2900     4000    4.5062193   0.28274334 
-    3000     4000    5.3409521   0.31415927 
-    3100     4000    6.0165991   0.34557519 
-    3200     4000     6.606767   0.37699112 
-    3300     4000    7.3997751   0.40840704 
-    3400     4000    8.1098807   0.43982297 
-    3500     4000    8.6552424    0.4712389 
-    3600     4000    9.8445204   0.50265482 
-    3700     4000    10.098753   0.53407075 
-    3800     4000    10.039489   0.56548668 
-    3900     4000    9.6376278    0.5969026 
-    4000     4000    9.2598836   0.62831853 
-    4100     4000    8.7116037   0.65973446 
-    4200     4000    8.1274117   0.69115038 
-    4300     4000    7.1487627   0.72256631 
-    4400     4000    6.2253778   0.75398224 
-    4500     4000    5.3061398   0.78539816 
-    4600     4000    4.4319316   0.81681409 
-    4700     4000     4.205607   0.84823002 
-    4800     4000    3.2112987   0.87964594 
-    4900     4000    2.6449777   0.91106187 
-    5000     4000    2.3475497    0.9424778 
-Loop time of 32.4926 on 1 procs for 3000 steps with 4000 atoms
-
-Performance: 7977.205 tau/day, 92.329 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 8.0124     | 8.0124     | 8.0124     |   0.0 | 24.66
-Neigh   | 10.993     | 10.993     | 10.993     |   0.0 | 33.83
-Comm    | 0.86697    | 0.86697    | 0.86697    |   0.0 |  2.67
-Output  | 0.0021827  | 0.0021827  | 0.0021827  |   0.0 |  0.01
-Modify  | 12.367     | 12.367     | 12.367     |   0.0 | 38.06
-Other   |            | 0.2515     |            |       |  0.77
-
-Nlocal:        4000.00 ave        4000 max        4000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        318.000 ave         318 max         318 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        14807.0 ave       14807 max       14807 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 14807
-Ave neighs/atom = 3.7017500
-Neighbor list builds = 2189
-Dangerous builds = 1536
-Total wall time: 0:00:43

examples/granular/log.29Oct20.pour.drum.g++.4

@@ -1,271 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) into cylinder
-# 'turn' cylinder by changing direction of gravity, then rotate it.
-# This simulates a rotating drum powder characterization experiment.
-
-variable	name string rotating_drum_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 30
-variable	boxy equal 30
-variable	boxz equal 50
-
-variable	drum_rad equal ${boxx}*0.5
-variable	drum_rad equal 30*0.5
-variable	drum_height equal 20
-
-variable	xc equal 0.5*${boxx}
-variable	xc equal 0.5*30
-variable	yc equal 0.5*${boxx}
-variable	yc equal 0.5*30
-variable	zc equal 0.5*${boxz}
-variable	zc equal 0.5*50
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.4*${rhi}
-variable skin equal 0.4*0.5
-
-#############
-processors * * 1
-region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 30 0 ${boxz}
-region		boxreg block 0 30 0 30 0 50
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
-  2 by 2 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
-
-variable	theta equal 0
-
-region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
-region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
-
-region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 20 ${boxz}
-region		insreg cylinder z 15 15 14.45 20 50
-
-fix		0 all balance 100 1.0 shift xy 5 1.1
-fix		1 all nve/sphere
-fix		grav all gravity 10 vector 0 0 -1
-fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
-fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
-
-comm_modify	vel yes
-
-neighbor	${skin} bin
-neighbor	0.2 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
-fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
-
-thermo_style	custom step atoms ke v_theta
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-#For removal later
-compute		1 all property/atom radius
-variable	zmax atom z+c_1>0.5*${drum_height}
-variable	zmax atom z+c_1>0.5*20
-group		delgroup dynamic all var zmax every 10000
-dynamic group delgroup defined
-
-run		2000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 50 50 84
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair granular, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
-Step Atoms KinEng v_theta 
-       0        0           -0            0 
-     100     4000           -0            0 
-     200     4000           -0            0 
-     300     4000           -0            0 
-     400     4000           -0            0 
-     500     4000           -0            0 
-     600     4000           -0            0 
-     700     4000           -0            0 
-     800     4000           -0            0 
-     900     4000           -0            0 
-    1000     4000           -0            0 
-    1100     4000           -0            0 
-    1200     4000           -0            0 
-    1300     4000           -0            0 
-    1400     4000           -0            0 
-    1500     4000           -0            0 
-    1600     4000           -0            0 
-    1700     4000           -0            0 
-    1800     4000           -0            0 
-    1900     4000           -0            0 
-    2000     4000           -0            0 
-Loop time of 3.86825 on 4 procs for 2000 steps with 4000 atoms
-
-Performance: 44671.398 tau/day, 517.030 timesteps/s
-96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.26114    | 0.27918    | 0.28728    |   2.0 |  7.22
-Neigh   | 1.2044     | 1.2414     | 1.3105     |   3.7 | 32.09
-Comm    | 0.38592    | 0.47065    | 0.51052    |   7.4 | 12.17
-Output  | 0.0007236  | 0.0013456  | 0.0024846  |   1.8 |  0.03
-Modify  | 1.6217     | 1.6723     | 1.7801     |   5.0 | 43.23
-Other   |            | 0.2034     |            |       |  5.26
-
-Nlocal:        1000.00 ave        1012 max         988 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        269.250 ave         278 max         256 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Neighs:        2060.50 ave        2156 max        1921 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 8242
-Ave neighs/atom = 2.0605000
-Neighbor list builds = 1004
-Dangerous builds = 4
-
-#Remove any particles that are above z > 0.5*drum_height
-delete_atoms	group delgroup
-Deleted 0 atoms, new total = 4000
-
-#Add top lid
-region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
-fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
-
-# 'Turn' drum by switching the direction of gravity
-unfix		grav
-unfix		ins1
-unfix		ins2
-fix		grav all gravity 10 vector 0 -1 0
-
-variable	theta equal 2*PI*elapsed/20000.0
-run		3000
-Per MPI rank memory allocation (min/avg/max) = 18.55 | 18.55 | 18.55 Mbytes
-Step Atoms KinEng v_theta 
-    2000     4000    65.819213            0 
-    2100     4000    105.02389  0.031415927 
-    2200     4000    112.02469  0.062831853 
-    2300     4000    92.271262   0.09424778 
-    2400     4000    89.369506   0.12566371 
-    2500     4000    80.910925   0.15707963 
-    2600     4000    31.620722   0.18849556 
-    2700     4000    4.3019937   0.21991149 
-    2800     4000    3.9913967   0.25132741 
-    2900     4000    4.5203726   0.28274334 
-    3000     4000     5.484886   0.31415927 
-    3100     4000    6.1085958   0.34557519 
-    3200     4000    6.7085635   0.37699112 
-    3300     4000    7.4787777   0.40840704 
-    3400     4000    8.2116413   0.43982297 
-    3500     4000    8.7979302    0.4712389 
-    3600     4000     9.871649   0.50265482 
-    3700     4000    10.012426   0.53407075 
-    3800     4000    9.9067754   0.56548668 
-    3900     4000     9.725458    0.5969026 
-    4000     4000    9.3350056   0.62831853 
-    4100     4000    8.8337295   0.65973446 
-    4200     4000    8.2712493   0.69115038 
-    4300     4000    6.9609934   0.72256631 
-    4400     4000    6.0120294   0.75398224 
-    4500     4000    5.0490036   0.78539816 
-    4600     4000    4.2796544   0.81681409 
-    4700     4000    4.1736483   0.84823002 
-    4800     4000    3.0860106   0.87964594 
-    4900     4000    2.6670909   0.91106187 
-    5000     4000    2.2901814    0.9424778 
-Loop time of 10.7627 on 4 procs for 3000 steps with 4000 atoms
-
-Performance: 24083.252 tau/day, 278.741 timesteps/s
-97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.6731     | 2.0701     | 2.3327     |  18.9 | 19.23
-Neigh   | 2.7389     | 3.1706     | 3.5146     |  15.7 | 29.46
-Comm    | 0.93507    | 1.5441     | 2.1182     |  39.1 | 14.35
-Output  | 0.0021682  | 0.0044412  | 0.006026   |   2.2 |  0.04
-Modify  | 3.0031     | 3.4223     | 3.9262     |  18.3 | 31.80
-Other   |            | 0.5511     |            |       |  5.12
-
-Nlocal:        1000.00 ave        1277 max         723 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        569.750 ave         809 max         454 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Neighs:        3690.50 ave        4937 max        2426 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 14762
-Ave neighs/atom = 3.6905000
-Neighbor list builds = 2187
-Dangerous builds = 1610
-Total wall time: 0:00:14

examples/granular/log.29Oct20.pour.flatwall.g++.1

@@ -1,188 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) on flat wall
-
-variable   	name string pour_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 20
-variable	boxy equal 20
-variable	boxz equal 30
-
-variable	xc1 equal 0.3*${boxx}
-variable	xc1 equal 0.3*20
-variable	xc2 equal 0.7*${boxx}
-variable	xc2 equal 0.7*20
-variable	yc equal 0.5*${boxy}
-variable	yc equal 0.5*20
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.3*${rhi}
-variable skin equal 0.3*0.5
-
-#############
-processors	* * 1
-region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 30
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
-  1 by 1 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
-pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
-
-comm_modify 	vel yes
-
-region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 30
-region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 30
-
-fix		1 all nve/sphere
-fix		grav all gravity 10.0 vector 0 0 -1
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-
-neighbor	${skin} bin
-neighbor	0.15 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
-
-thermo_style	custom step atoms ke
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-run		5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.15
-  ghost atom cutoff = 1.15
-  binsize = 0.575, bins = 35 35 53
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair granular, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
-Step Atoms KinEng 
-       0        0           -0 
-     100      926           -0 
-     200      926           -0 
-     300      926           -0 
-     400     1498           -0 
-     500     1498           -0 
-     600     1498           -0 
-     700     2275           -0 
-     800     2275           -0 
-     900     2275           -0 
-    1000     2275           -0 
-    1100     2954           -0 
-    1200     2954           -0 
-    1300     2954           -0 
-    1400     3000           -0 
-    1500     3000           -0 
-    1600     3000           -0 
-    1700     3000           -0 
-    1800     3000           -0 
-    1900     3000           -0 
-    2000     3000           -0 
-    2100     3000           -0 
-    2200     3000           -0 
-    2300     3000           -0 
-    2400     3000           -0 
-    2500     3000           -0 
-    2600     3000           -0 
-    2700     3000           -0 
-    2800     3000           -0 
-    2900     3000           -0 
-    3000     3000           -0 
-    3100     3000           -0 
-    3200     3000           -0 
-    3300     3000           -0 
-    3400     3000           -0 
-    3500     3000           -0 
-    3600     3000           -0 
-    3700     3000           -0 
-    3800     3000           -0 
-    3900     3000           -0 
-    4000     3000           -0 
-    4100     3000           -0 
-    4200     3000           -0 
-    4300     3000           -0 
-    4400     3000           -0 
-    4500     3000           -0 
-    4600     3000           -0 
-    4700     3000           -0 
-    4800     3000           -0 
-    4900     3000           -0 
-    5000     3000           -0 
-Loop time of 24.3889 on 1 procs for 5000 steps with 3000 atoms
-
-Performance: 17713.003 tau/day, 205.012 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 14.362     | 14.362     | 14.362     |   0.0 | 58.89
-Neigh   | 3.3483     | 3.3483     | 3.3483     |   0.0 | 13.73
-Comm    | 0.42893    | 0.42893    | 0.42893    |   0.0 |  1.76
-Output  | 0.0025065  | 0.0025065  | 0.0025065  |   0.0 |  0.01
-Modify  | 6.059      | 6.059      | 6.059      |   0.0 | 24.84
-Other   |            | 0.1876     |            |       |  0.77
-
-Nlocal:        3000.00 ave        3000 max        3000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        462.000 ave         462 max         462 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        17694.0 ave       17694 max       17694 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 17694
-Ave neighs/atom = 5.8980000
-Neighbor list builds = 1133
-Dangerous builds = 0
-Total wall time: 0:00:24

examples/granular/log.29Oct20.pour.flatwall.g++.4

@@ -1,188 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) on flat wall
-
-variable   	name string pour_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 20
-variable	boxy equal 20
-variable	boxz equal 30
-
-variable	xc1 equal 0.3*${boxx}
-variable	xc1 equal 0.3*20
-variable	xc2 equal 0.7*${boxx}
-variable	xc2 equal 0.7*20
-variable	yc equal 0.5*${boxy}
-variable	yc equal 0.5*20
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.3*${rhi}
-variable skin equal 0.3*0.5
-
-#############
-processors	* * 1
-region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 30
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
-  2 by 2 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
-pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
-
-comm_modify 	vel yes
-
-region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 30
-region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 30
-
-fix		1 all nve/sphere
-fix		grav all gravity 10.0 vector 0 0 -1
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-
-neighbor	${skin} bin
-neighbor	0.15 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
-
-thermo_style	custom step atoms ke
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-run		5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.15
-  ghost atom cutoff = 1.15
-  binsize = 0.575, bins = 35 35 53
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair granular, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
-Step Atoms KinEng 
-       0        0           -0 
-     100      926           -0 
-     200      926           -0 
-     300      926           -0 
-     400     1498           -0 
-     500     1498           -0 
-     600     1498           -0 
-     700     2275           -0 
-     800     2275           -0 
-     900     2275           -0 
-    1000     2275           -0 
-    1100     2954           -0 
-    1200     2954           -0 
-    1300     2954           -0 
-    1400     3000           -0 
-    1500     3000           -0 
-    1600     3000           -0 
-    1700     3000           -0 
-    1800     3000           -0 
-    1900     3000           -0 
-    2000     3000           -0 
-    2100     3000           -0 
-    2200     3000           -0 
-    2300     3000           -0 
-    2400     3000           -0 
-    2500     3000           -0 
-    2600     3000           -0 
-    2700     3000           -0 
-    2800     3000           -0 
-    2900     3000           -0 
-    3000     3000           -0 
-    3100     3000           -0 
-    3200     3000           -0 
-    3300     3000           -0 
-    3400     3000           -0 
-    3500     3000           -0 
-    3600     3000           -0 
-    3700     3000           -0 
-    3800     3000           -0 
-    3900     3000           -0 
-    4000     3000           -0 
-    4100     3000           -0 
-    4200     3000           -0 
-    4300     3000           -0 
-    4400     3000           -0 
-    4500     3000           -0 
-    4600     3000           -0 
-    4700     3000           -0 
-    4800     3000           -0 
-    4900     3000           -0 
-    5000     3000           -0 
-Loop time of 12.1982 on 4 procs for 5000 steps with 3000 atoms
-
-Performance: 35414.923 tau/day, 409.895 timesteps/s
-97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.7141     | 3.8131     | 6.2143     | 107.3 | 31.26
-Neigh   | 0.77648    | 0.96585    | 1.1892     |  18.3 |  7.92
-Comm    | 0.7427     | 3.5566     | 5.9731     | 128.4 | 29.16
-Output  | 0.0067544  | 0.0086352  | 0.011408   |   1.8 |  0.07
-Modify  | 3.3476     | 3.5826     | 3.8235     |  11.5 | 29.37
-Other   |            | 0.2715     |            |       |  2.23
-
-Nlocal:        750.000 ave        1033 max         463 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        435.000 ave         492 max         378 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:        4434.50 ave        7028 max        1967 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 17738
-Ave neighs/atom = 5.9126667
-Neighbor list builds = 1139
-Dangerous builds = 0
-Total wall time: 0:00:12

src/.gitignore

@@ -462,8 +462,6 @@
 /atom_vec_full.h
 /atom_vec_full_hars.cpp
 /atom_vec_full_hars.h
-/atom_vec_granular.cpp
-/atom_vec_granular.h
 /atom_vec_molecular.cpp
 /atom_vec_molecular.h
 /atom_vec_oxdna.cpp
@@ -1573,6 +1571,8 @@
 /fix_srp.h
 /fix_srp_react.cpp
 /fix_srp_react.h
+/fix_heat_flow.cpp
+/fix_heat_flow.h
 /fix_tfmc.cpp
 /fix_tfmc.h
 /fix_ttm.cpp
@@ -1581,6 +1581,22 @@
 /fix_ttm_grid.h
 /fix_ttm_mod.cpp
 /fix_ttm_mod.h
+/granular_model.cpp
+/granular_model.h
+/gran_sub_mod_normal.cpp
+/gran_sub_mod_normal.h
+/gran_sub_mod_damping.cpp
+/gran_sub_mod_damping.h
+/gran_sub_mod_tangential.cpp
+/gran_sub_mod_tangential.h
+/gran_sub_mod_twisting.cpp
+/gran_sub_mod_twisting.h
+/gran_sub_mod_rolling.cpp
+/gran_sub_mod_rolling.h
+/gran_sub_mod_heat.cpp
+/gran_sub_mod_heat.h
+/gran_sub_mod.cpp
+/gran_sub_mod.h
 /pair_born_coul_long_cs.cpp
 /pair_born_coul_long_cs.h
 /pair_born_coul_dsf_cs.cpp

src/GRANULAR/fix_heat_flow.cpp

@@ -0,0 +1,238 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "fix_heat_flow.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "respa.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum {NONE, CONSTANT, TYPE};
+
+/* ---------------------------------------------------------------------- */
+
+FixHeatFlow::FixHeatFlow(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg < 4) error->all(FLERR,"Illegal fix command");
+
+  cp_style = NONE;
+  comm_forward = 1;
+  comm_reverse = 1;
+
+  int ntypes = atom->ntypes;
+  if (strcmp(arg[3],"constant") == 0) {
+    if (narg != 5) error->all(FLERR,"Illegal fix command");
+    cp_style = CONSTANT;
+    cp = utils::numeric(FLERR,arg[4],false,lmp);
+    if (cp < 0.0) error->all(FLERR,"Illegal fix command");
+  } else if (strcmp(arg[3],"type") == 0) {
+    if (narg != 4 + ntypes) error->all(FLERR,"Illegal fix command");
+    cp_style = TYPE;
+    memory->create(cp_type,ntypes+1,"fix/temp/integrate:cp_type");
+    for (int i = 1; i <= ntypes; i++) {
+      cp_type[i] = utils::numeric(FLERR,arg[3+i],false,lmp);
+      if (cp_type[i] < 0.0) error->all(FLERR,"Illegal fix command");
+    }
+  } else {
+    error->all(FLERR,"Illegal fix command");
+  }
+
+  if (cp_style == NONE)
+    error->all(FLERR, "Must specify specific heat in fix temp/integrate");
+  dynamic_group_allow = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixHeatFlow::setmask()
+{
+  int mask = 0;
+  mask |= PRE_FORCE;
+  mask |= FINAL_INTEGRATE;
+  mask |= FINAL_INTEGRATE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::init()
+{
+  dt = update->dt;
+
+  if (!atom->temperature_flag)
+    error->all(FLERR,"Fix temp/integrate requires atom style with temperature property");
+  if (!atom->heatflow_flag)
+    error->all(FLERR,"Fix temp/integrate requires atom style with heatflow property");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::setup(int /*vflag*/)
+{
+  // Identify whether this is the first instance of fix heat/flow
+  first_flag = 0;
+
+  int i = 0;
+  auto fixlist = modify->get_fix_by_style("heat/flow");
+  for (const auto &ifix : fixlist) {
+    if (strcmp(ifix->id, id) == 0) break;
+    i++;
+  }
+
+  if (i == 0) first_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::setup_pre_force(int /*vflag*/)
+{
+  pre_force(0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::pre_force(int /*vflag*/)
+{
+  // send updated temperatures to ghosts if first instance of fix
+  // then clear heatflow for next force calculation
+  double *heatflow = atom->heatflow;
+  if (first_flag) {
+    comm->forward_comm(this);
+    for (int i = 0; i < atom->nmax; i++) heatflow[i] = 0.0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::final_integrate()
+{
+  // update temperature of atoms in group
+
+  double *temperature = atom->temperature;
+  double *heatflow = atom->heatflow;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // add ghost contributions to heatflow if first instance of fix
+  if (first_flag)
+    comm->reverse_comm(this);
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        temperature[i] += dt * heatflow[i] / (calc_cp(i) * rmass[i]);
+      }
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        temperature[i] += dt * heatflow[i] / (calc_cp(i) * mass[type[i]]);
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::final_integrate_respa(int /*ilevel*/, int /*iloop*/)
+{
+  dt = update->dt;
+  final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::reset_dt()
+{
+  dt = update->dt;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixHeatFlow::calc_cp(int i)
+{
+  if (cp_style == TYPE) {
+    return cp_type[atom->type[i]];
+  } else {
+    return cp;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixHeatFlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
+{
+  int i, j, m;
+
+  double *temperature = atom->temperature;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    buf[m++] = temperature[j];
+  }
+
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::unpack_forward_comm(int n, int first, double *buf)
+{
+  int i, m, last;
+
+  m = 0;
+  last = first + n;
+
+  double *temperature = atom->temperature;
+
+  for (i = first; i < last; i++) temperature[i] = buf[m++];
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixHeatFlow::pack_reverse_comm(int n, int first, double *buf)
+{
+  int m = 0;
+  int last = first + n;
+  double *heatflow = atom->heatflow;
+
+  for (int i = first; i < last; i++) {
+    buf[m++] = heatflow[i];
+  }
+
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixHeatFlow::unpack_reverse_comm(int n, int *list, double *buf)
+{
+  int m = 0;
+  double *heatflow = atom->heatflow;
+
+  for (int i = 0; i < n; i++)
+    heatflow[list[i]] += buf[m++];
+}

src/GRANULAR/fix_heat_flow.h

@@ -0,0 +1,56 @@
+/* -*- 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 FIX_CLASS
+// clang-format off
+FixStyle(heat/flow,FixHeatFlow);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_HEAT_FLOW_H
+#define LMP_FIX_HEAT_FLOW_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixHeatFlow : public Fix {
+ public:
+  FixHeatFlow(class LAMMPS *, int, char **);
+
+  int setmask() override;
+  void init() override;
+  void setup(int) override;
+  void setup_pre_force(int) override;
+  void pre_force(int) override;
+  void final_integrate() override;
+  void final_integrate_respa(int, int) override;
+  int pack_forward_comm(int, int *, double *, int, int *) override;
+  void unpack_forward_comm(int, int, double *) override;
+  int pack_reverse_comm(int, int, double *) override;
+  void unpack_reverse_comm(int, int *, double *) override;
+  void reset_dt() override;
+
+ protected:
+  double dt;
+  double cp, *cp_type;
+  int cp_style;
+  int first_flag;
+
+  double calc_cp(int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/GRANULAR/fix_pour.cpp

@@ -270,6 +270,7 @@ FixPour::~FixPour()
   delete[] molfrac;
   delete[] idrigid;
   delete[] idshake;
+  delete[] idregion;
   delete[] radius_poly;
   delete[] frac_poly;
   memory->destroy(coords);

src/GRANULAR/fix_wall_gran.h

@@ -20,15 +20,17 @@ FixStyle(wall/gran,FixWallGran);
 #ifndef LMP_FIX_WALL_GRAN_H
 #define LMP_FIX_WALL_GRAN_H
 
+#include "granular_model.h"
 #include "fix.h"
 
 namespace LAMMPS_NS {
 
+namespace Granular_NS {
+  class GranularModel;
+}
+
 class FixWallGran : public Fix {
  public:
-  enum { HOOKE, HOOKE_HISTORY, HERTZ_HISTORY, GRANULAR };
-  enum { NORMAL_NONE, NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR };
-
   FixWallGran(class LAMMPS *, int, char **);
   ~FixWallGran() override;
   int setmask() override;
@@ -49,54 +51,27 @@ class FixWallGran : public Fix {
   int maxsize_restart() override;
   void reset_dt() override;
 
-  void hooke(double, double, double, double, double *, double *, double *, double *, double *,
-             double, double, double *);
-  void hooke_history(double, double, double, double, double *, double *, double *, double *,
-                     double *, double, double, double *, double *);
-  void hertz_history(double, double, double, double, double *, double, double *, double *, double *,
-                     double *, double, double, double *, double *);
-  void granular(double, double, double, double, double *, double, double *, double *, double *,
-                double *, double, double, double *, double *);
-
-  double pulloff_distance(double);
-
  protected:
   int wallstyle, wiggle, wshear, axis;
-  int pairstyle, nlevels_respa;
+  int nlevels_respa;
   bigint time_origin;
-  double kn, kt, gamman, gammat, xmu;
 
   // for granular model choices
-  int normal_model, damping_model;
-  int tangential_model, roll_model, twist_model;
-  int limit_damping;
-
-  // history flags
-  int normal_history, tangential_history, roll_history, twist_history;
-
-  // indices of history entries
-  int normal_history_index;
-  int tangential_history_index;
-  int roll_history_index;
-  int twist_history_index;
-
-  // material coefficients
-  double Emod, poiss, Gmod;
-
-  // contact model coefficients
-  double normal_coeffs[4];
-  double tangential_coeffs[3];
-  double roll_coeffs[3];
-  double twist_coeffs[3];
+  class Granular_NS::GranularModel *model;
 
   double lo, hi, cylradius;
   double amplitude, period, omega, vshear;
   double dt;
+  double Twall;
   char *idregion;
 
   int use_history;       // if particle/wall interaction stores history
   int history_update;    // flag for whether shear history is updated
   int size_history;      // # of shear history values per contact
+  int heat_flag;
+
+  int tvar;
+  char *tstr;
 
   // shear history for single contact per particle
 

src/GRANULAR/fix_wall_gran_region.cpp

@@ -12,23 +12,29 @@
    ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing authors: Dan Bolintineanu (SNL)
+   Contributing authors: Dan Bolintineanu (SNL), Joel Clemmer (SNL)
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_gran_region.h"
 
 #include "atom.h"
+#include "granular_model.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
+#include "input.h"
 #include "memory.h"
 #include "neighbor.h"
+#include "math_extra.h"
 #include "region.h"
 #include "update.h"
+#include "variable.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathExtra;
 
 /* ---------------------------------------------------------------------- */
 
@@ -45,6 +51,8 @@ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) :
   tmax = region->tmax;
   c2r = new int[tmax];
 
+  model->contact_type = WALLREGION;
+
   // re-allocate atom-based arrays with nshear
   // do not register with Atom class, since parent class did that
 
@@ -116,13 +124,17 @@ void FixWallGranRegion::init()
 void FixWallGranRegion::post_force(int /*vflag*/)
 {
   int i, m, nc, iwall;
-  double dx, dy, dz, rsq, meff;
+  double dx, dy, dz, meff;
+  double *forces, *torquesi;
   double vwall[3];
+  double w0[3] = {0.0};
+  bool touchflag = false;
 
   // do not update shear history during setup
 
   history_update = 1;
   if (update->setupflag) history_update = 0;
+  model->history_update = history_update;
 
   // if just reneighbored:
   // update rigid body masses for owned atoms if using FixRigid
@@ -157,7 +169,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-
+  double *temperature, *heatflow;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -169,97 +181,112 @@ void FixWallGranRegion::post_force(int /*vflag*/)
     region->set_velocity();
   }
 
-  if (peratom_flag) { clear_stored_contacts(); }
+  if (peratom_flag) clear_stored_contacts();
+
+  // Define constant wall properties (atom j)
+  model->radj = 0.0;
+  model->omegaj = w0;
+  if (heat_flag) {
+    temperature = atom->temperature;
+    heatflow = atom->heatflow;
+    if (tstr)
+      Twall = input->variable->compute_equal(tvar);
+    model->Tj = Twall;
+  }
 
   for (i = 0; i < nlocal; i++) {
-    if (mask[i] & groupbit) {
-      if (!region->match(x[i][0], x[i][1], x[i][2])) continue;
+    if ((!mask[i]) & groupbit) continue;
+    if (! region->match(x[i][0], x[i][1], x[i][2])) continue;
 
-      if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) {
-        nc = region->surface(x[i][0], x[i][1], x[i][2], radius[i] + pulloff_distance(radius[i]));
-      } else {
-        nc = region->surface(x[i][0], x[i][1], x[i][2], radius[i]);
+    nc = region->surface(x[i][0], x[i][1], x[i][2], model->pulloff_distance(radius[i], 0.0));
+    if (nc > tmax) error->one(FLERR, "Too many wallgran/region contacts for one particle");
+
+    // shear history maintenance
+    // update ncontact,walls,shear2many for particle I
+    //   to reflect new and persistent shear historyvalues
+    // also set c2r[] = indices into region->contact[]for each of N contacts
+    // process zero or one contact here, otherwiseinvoke update_contacts()
+
+    if (use_history) {
+      if (nc == 0) {
+        ncontact[i] = 0;
+        continue;
       }
-      if (nc > tmax) error->one(FLERR, "Too many wall/gran/region contacts for one particle");
-
-      // shear history maintenance
-      // update ncontact,walls,shear2many for particle I
-      //   to reflect new and persistent shear history values
-      // also set c2r[] = indices into region->contact[] for each of N contacts
-      // process zero or one contact here, otherwise invoke update_contacts()
-
-      if (use_history) {
-        if (nc == 0) {
-          ncontact[i] = 0;
-          continue;
-        }
-        if (nc == 1) {
-          c2r[0] = 0;
-          iwall = region->contact[0].iwall;
-          if (ncontact[i] == 0) {
-            ncontact[i] = 1;
-            walls[i][0] = iwall;
-            for (m = 0; m < size_history; m++) history_many[i][0][m] = 0.0;
-          } else if (ncontact[i] > 1 || iwall != walls[i][0])
-            update_contacts(i, nc);
-        } else
+      if (nc == 1) {
+        c2r[0] = 0;
+        iwall = region->contact[0].iwall;
+        if (ncontact[i] == 0) {
+          ncontact[i] = 1;
+          walls[i][0] = iwall;
+          for (m = 0; m < size_history; m++) history_many[i][0][m] = 0.0;
+        } else if (ncontact[i] > 1 || iwall != walls[i][0])
           update_contacts(i, nc);
+      } else
+        update_contacts(i, nc);
+    }
+
+    // process current contacts
+    for (int ic = 0; ic < nc; ic++) {
+
+      // Reset model and copy initial geometric data
+      model->dx[0] = region->contact[ic].delx;
+      model->dx[1] = region->contact[ic].dely;
+      model->dx[2] = region->contact[ic].delz;
+      model->radi = radius[i];
+      model->radj = region->contact[ic].radius;
+      model->r = region->contact[ic].r;
+      if (model->beyond_contact) model->touch = history_many[i][c2r[ic]][0];
+
+      touchflag = model->check_contact();
+
+      if (!touchflag) {
+        if (use_history)
+          for (m = 0; m < size_history; m++)
+            history_many[i][c2r[ic]][m] = 0.0;
+        continue;
       }
 
-      // process current contacts
-      for (int ic = 0; ic < nc; ic++) {
+      if (model->beyond_contact)
+        history_many[i][c2r[ic]][0] = 1;
 
-        // rsq = squared contact distance
-        // xc = contact point
+      if (regiondynamic) region->velocity_contact(vwall, x[i], ic);
+      model->vj = vwall;
 
-        rsq = region->contact[ic].r * region->contact[ic].r;
+      // meff = effective mass of sphere
+      // if I is part of rigid body, use body mass
 
-        if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) {
-          if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i] * radius[i]) {
-            for (m = 0; m < size_history; m++) history_many[i][0][m] = 0.0;
-            continue;
-          }
-        }
+      meff = rmass[i];
+      if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
 
-        dx = region->contact[ic].delx;
-        dy = region->contact[ic].dely;
-        dz = region->contact[ic].delz;
+      // Copy additional information and prepare force calculations
+      model->meff = meff;
+      model->vi = v[i];
+      model->omegai = omega[i];
 
-        if (regiondynamic) region->velocity_contact(vwall, x[i], ic);
+      if (use_history) model->history = history_many[i][c2r[ic]];
+      if (heat_flag) model->Ti = temperature[i];
 
-        // meff = effective mass of sphere
-        // if I is part of rigid body, use body mass
+      model->calculate_forces();
 
-        meff = rmass[i];
-        if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
+      forces = model->forces;
+      torquesi = model->torquesi;
 
-        // store contact info
-        if (peratom_flag) {
-          array_atom[i][0] = 1.0;
-          array_atom[i][4] = x[i][0] - dx;
-          array_atom[i][5] = x[i][1] - dy;
-          array_atom[i][6] = x[i][2] - dz;
-          array_atom[i][7] = radius[i];
-        }
+      // apply forces & torques
+      add3(f[i], forces, f[i]);
 
-        // invoke sphere/wall interaction
-        double *contact;
-        if (peratom_flag)
-          contact = array_atom[i];
-        else
-          contact = nullptr;
+      add3(torque[i], torquesi, torque[i]);
+      if (heat_flag) heatflow[i] += model->dq;
 
-        if (pairstyle == FixWallGran::HOOKE)
-          hooke(rsq, dx, dy, dz, vwall, v[i], f[i], omega[i], torque[i], radius[i], meff, contact);
-        else if (pairstyle == FixWallGran::HOOKE_HISTORY)
-          hooke_history(rsq, dx, dy, dz, vwall, v[i], f[i], omega[i], torque[i], radius[i], meff,
-                        history_many[i][c2r[ic]], contact);
-        else if (pairstyle == FixWallGran::HERTZ_HISTORY)
-          hertz_history(rsq, dx, dy, dz, vwall, region->contact[ic].radius, v[i], f[i], omega[i],
-                        torque[i], radius[i], meff, history_many[i][c2r[ic]], contact);
-        else if (pairstyle == FixWallGran::GRANULAR)
-          granular(rsq, dx, dy, dz, vwall, region->contact[ic].radius, v[i], f[i], omega[i],
-                   torque[i], radius[i], meff, history_many[i][c2r[ic]], contact);
+      // store contact info
+      if (peratom_flag) {
+        array_atom[i][0] = 1.0;
+        array_atom[i][1] = forces[0];
+        array_atom[i][2] = forces[1];
+        array_atom[i][3] = forces[2];
+        array_atom[i][4] = x[i][0] - dx;
+        array_atom[i][5] = x[i][1] - dy;
+        array_atom[i][6] = x[i][2] - dz;
+        array_atom[i][7] = radius[i];
       }
     }
   }

src/GRANULAR/gran_sub_mod.cpp

@@ -0,0 +1,128 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This class contains a framework for granular sub models (GranSubMod):
+   normal, damping, tangential, rolling, twisting, and heat
+   These are used to calculate forces/torques/etc based on contact geometry
+
+   Contributing authors:
+   Dan Bolintineanu (SNL), Joel Clemmer (SNL)
+----------------------------------------------------------------------- */
+
+#include "gran_sub_mod.h"
+#include "error.h"
+#include "utils.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+
+/* ----------------------------------------------------------------------
+   Parent class for all types of granular sub models
+------------------------------------------------------------------------- */
+
+GranSubMod::GranSubMod(class GranularModel *gm, LAMMPS *lmp) : Pointers(lmp)
+{
+  this->gm = gm;
+
+  allocated = 0;
+  size_history = 0;
+  history_index = 0;
+  allow_cohesion = 1;
+  beyond_contact = 0;
+  num_coeffs = 0;
+  area_flag = 0;
+
+  nondefault_history_transfer = 0;
+  transfer_history_factor = nullptr;
+  coeffs = nullptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+GranSubMod::~GranSubMod()
+{
+  if (allocated) delete [] coeffs;
+  delete [] transfer_history_factor;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubMod::allocate_coeffs()
+{
+  allocated = 1;
+  coeffs = new double[num_coeffs];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubMod::mix_coeffs(double* icoeffs, double* jcoeffs)
+{
+  for (int i = 0; i < num_coeffs; i++)
+    coeffs[i] = mix_geom(icoeffs[i], jcoeffs[i]);
+  coeffs_to_local();
+}
+
+/* ----------------------------------------------------------------------
+   mixing of Young's modulus (E)
+------------------------------------------------------------------------- */
+
+double GranSubMod::mix_stiffnessE(double E1, double E2,
+                                    double poiss1, double poiss2)
+{
+  double factor1 = (1 - poiss1 * poiss1) / E1;
+  double factor2 = (1 - poiss2 * poiss2) / E2;
+  return 1 / (factor1 + factor2);
+}
+
+/* ----------------------------------------------------------------------
+   mixing of shear modulus (G)
+------------------------------------------------------------------------ */
+
+double GranSubMod::mix_stiffnessG(double E1, double E2,
+                                    double poiss1, double poiss2)
+{
+  double factor1 = 2 * (2 - poiss1) * (1 + poiss1) / E1;
+  double factor2 = 2 * (2 - poiss2) * (1 + poiss2) / E2;
+  return 1 / (factor1 + factor2);
+}
+
+/* ----------------------------------------------------------------------
+   mixing of Young's modulus (E) for walls
+------------------------------------------------------------------------- */
+
+double GranSubMod::mix_stiffnessE_wall(double E, double poiss)
+{
+  double factor = 2 * (1 - poiss * poiss);
+  return E / factor;
+}
+
+/* ----------------------------------------------------------------------
+   mixing of shear modulus (G) for walls
+------------------------------------------------------------------------ */
+
+double GranSubMod::mix_stiffnessG_wall(double E, double poiss)
+{
+  double factor = 4.0 * (2 - poiss) * (1 + poiss);
+  return E / factor;
+}
+
+/* ----------------------------------------------------------------------
+   mixing of everything else
+------------------------------------------------------------------------- */
+
+double GranSubMod::mix_geom(double val1, double val2)
+{
+  return sqrt(val1 * val2);
+}

src/GRANULAR/gran_sub_mod.h

@@ -0,0 +1,62 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_GRAN_SUB_MOD_H
+#define LMP_GRAN_SUB_MOD_H
+
+#include "granular_model.h"
+#include "pointers.h"    // IWYU pragma: export
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubMod : protected Pointers {
+ public:
+  GranSubMod(class GranularModel *, class LAMMPS *);
+  virtual ~GranSubMod();
+
+  int num_coeffs;
+  double *coeffs;
+  void read_restart();
+  virtual void mix_coeffs(double*, double*);
+  virtual void coeffs_to_local() {};
+  virtual void init() {}; // called after all sub models + coeffs defined
+
+  void allocate_coeffs();
+  std::string name;
+
+  int size_history;
+  int nondefault_history_transfer;
+  double *transfer_history_factor;
+
+  int history_index;
+  int beyond_contact;  // If the sub model contact extends beyond overlap
+  int allow_cohesion;  // If the sub model works with a cohesive normal force
+  int area_flag;       // If the sub model requires area
+
+  GranularModel *gm;
+
+ protected:
+  int allocated;
+
+  double mix_stiffnessE(double, double, double, double);
+  double mix_stiffnessG(double, double, double, double);
+  double mix_stiffnessE_wall(double, double);
+  double mix_stiffnessG_wall(double, double);
+  double mix_geom(double, double);
+};
+
+}    // namespace GranularModel
+}    // namespace LAMMPS_NS
+
+#endif /* GRAN_SUB_MOD_H */

src/GRANULAR/gran_sub_mod_damping.cpp

@@ -0,0 +1,121 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_damping.h"
+#include "gran_sub_mod_normal.h"
+#include "granular_model.h"
+#include "math_special.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathSpecial;
+
+/* ----------------------------------------------------------------------
+   Default damping model
+------------------------------------------------------------------------- */
+
+GranSubModDamping::GranSubModDamping(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModDamping::init()
+{
+  damp = gm->normal_model->damp;
+}
+
+/* ----------------------------------------------------------------------
+   No model
+------------------------------------------------------------------------- */
+
+GranSubModDampingNone::GranSubModDampingNone(GranularModel *gm, LAMMPS *lmp) : GranSubModDamping(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModDampingNone::calculate_forces()
+{
+  damp_prefactor = 0.0;
+  return 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   Velocity damping
+------------------------------------------------------------------------- */
+
+GranSubModDampingVelocity::GranSubModDampingVelocity(GranularModel *gm, LAMMPS *lmp) : GranSubModDamping(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModDampingVelocity::calculate_forces()
+{
+  damp_prefactor = damp;
+  return -damp_prefactor * gm->vnnr;
+}
+
+/* ----------------------------------------------------------------------
+   Mass velocity damping
+------------------------------------------------------------------------- */
+
+GranSubModDampingMassVelocity::GranSubModDampingMassVelocity(GranularModel *gm, LAMMPS *lmp) : GranSubModDamping(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModDampingMassVelocity::calculate_forces()
+{
+  damp_prefactor = damp * gm->meff;
+  return -damp_prefactor * gm->vnnr;
+}
+
+/* ----------------------------------------------------------------------
+   Default, viscoelastic damping
+------------------------------------------------------------------------- */
+
+GranSubModDampingViscoelastic::GranSubModDampingViscoelastic(GranularModel *gm, LAMMPS *lmp) : GranSubModDamping(gm, lmp)
+{
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModDampingViscoelastic::calculate_forces()
+{
+  damp_prefactor = damp * gm->meff * gm->area;
+  return -damp_prefactor * gm->vnnr;
+}
+
+/* ----------------------------------------------------------------------
+   Tsuji damping
+------------------------------------------------------------------------- */
+
+GranSubModDampingTsuji::GranSubModDampingTsuji(GranularModel *gm, LAMMPS *lmp) : GranSubModDamping(gm, lmp)
+{
+  allow_cohesion = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModDampingTsuji::init()
+{
+  double tmp = gm->normal_model->damp;
+  damp = 1.2728 - 4.2783 * tmp + 11.087 * square(tmp);
+  damp += -22.348 * cube(tmp) + 27.467 * powint(tmp, 4);
+  damp += -18.022 * powint(tmp, 5) + 4.8218 * powint(tmp,6);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModDampingTsuji::calculate_forces()
+{
+  damp_prefactor = damp * sqrt(gm->meff * gm->Fnormal / gm->delta);
+  return -damp_prefactor * gm->vnnr;
+}

src/GRANULAR/gran_sub_mod_damping.h

@@ -0,0 +1,104 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModDampingNone,
+         DAMPING);
+
+GranSubModStyle(velocity,
+         GranSubModDampingVelocity,
+         DAMPING);
+
+GranSubModStyle(mass_velocity,
+         GranSubModDampingMassVelocity,
+         DAMPING);
+
+GranSubModStyle(viscoelastic,
+         GranSubModDampingViscoelastic,
+         DAMPING);
+
+GranSubModStyle(tsuji,
+         GranSubModDampingTsuji,
+         DAMPING);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_DAMPING_H
+#define GRAN_SUB_MOD_DAMPING_H
+
+#include "gran_sub_mod.h"
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModDamping : public GranSubMod {
+ public:
+  GranSubModDamping(class GranularModel *, class LAMMPS *);
+  ~GranSubModDamping() {};
+  virtual void init();
+  virtual double calculate_forces() = 0;
+  double damp_prefactor; // Used by tangential models
+ protected:
+  double damp;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModDampingNone : public GranSubModDamping {
+ public:
+  GranSubModDampingNone(class GranularModel *, class LAMMPS *);
+  void init() override {};
+  double calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModDampingVelocity : public GranSubModDamping {
+ public:
+  GranSubModDampingVelocity(class GranularModel *, class LAMMPS *);
+  double calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModDampingMassVelocity : public GranSubModDamping {
+ public:
+  GranSubModDampingMassVelocity(class GranularModel *, class LAMMPS *);
+  double calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModDampingViscoelastic : public GranSubModDamping {
+ public:
+  GranSubModDampingViscoelastic(class GranularModel *, class LAMMPS *);
+  double calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModDampingTsuji : public GranSubModDamping {
+ public:
+  GranSubModDampingTsuji(class GranularModel *, class LAMMPS *);
+  void init() override;
+  double calculate_forces();
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_DAMPING_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/gran_sub_mod_heat.cpp

@@ -0,0 +1,65 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_heat.h"
+#include "granular_model.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+
+/* ----------------------------------------------------------------------
+   Default heat conduction
+------------------------------------------------------------------------- */
+
+GranSubModHeat::GranSubModHeat(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   Area-based heat conduction
+------------------------------------------------------------------------- */
+
+GranSubModHeatNone::GranSubModHeatNone(GranularModel *gm, LAMMPS *lmp) : GranSubModHeat(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModHeatNone::calculate_heat()
+{
+  return 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   Area-based heat conduction
+------------------------------------------------------------------------- */
+
+GranSubModHeatArea::GranSubModHeatArea(GranularModel *gm, LAMMPS *lmp) : GranSubModHeat(gm, lmp)
+{
+  num_coeffs = 1;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModHeatArea::coeffs_to_local()
+{
+  conductivity = coeffs[0];
+
+  if (conductivity < 0.0) error->all(FLERR, "Illegal area heat model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModHeatArea::calculate_heat()
+{
+  return conductivity * gm->area * (gm->Tj - gm->Ti);
+}

src/GRANULAR/gran_sub_mod_heat.h

@@ -0,0 +1,64 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModHeatNone,
+         HEAT);
+
+GranSubModStyle(area,
+         GranSubModHeatArea,
+         HEAT);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_HEAT_H
+#define GRAN_SUB_MOD_HEAT_H
+
+#include "gran_sub_mod.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModHeat : public GranSubMod {
+ public:
+  GranSubModHeat(class GranularModel *, class LAMMPS *);
+  ~GranSubModHeat() {};
+  virtual double calculate_heat() = 0;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModHeatNone : public GranSubModHeat {
+ public:
+  GranSubModHeatNone(class GranularModel *, class LAMMPS *);
+  double calculate_heat();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModHeatArea : public GranSubModHeat {
+ public:
+  GranSubModHeatArea(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  double calculate_heat();
+ protected:
+  double conductivity;
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_HEAT_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/gran_sub_mod_normal.cpp

@@ -0,0 +1,353 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_normal.h"
+#include "granular_model.h"
+#include "error.h"
+#include "math_const.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathConst;
+
+#define PI27SQ 266.47931882941264802866    // 27*PI**2
+#define THREEROOT3 5.19615242270663202362  // 3*sqrt(3)
+#define SIXROOT6 14.69693845669906728801   // 6*sqrt(6)
+#define INVROOT6 0.40824829046386307274    // 1/sqrt(6)
+#define FOURTHIRDS (4.0/3.0)               // 4/3
+#define ONETHIRD (1.0/3.0)                 // 1/3
+#define THREEQUARTERS 0.75                 // 3/4
+
+/* ----------------------------------------------------------------------
+   Default normal model
+------------------------------------------------------------------------- */
+
+GranSubModNormal::GranSubModNormal(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp)
+{
+  material_properties = 0;
+  cohesive_flag = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+bool GranSubModNormal::touch()
+{
+  bool touchflag = (gm->rsq < gm->radsum * gm->radsum);
+  return touchflag;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormal::pulloff_distance(double radi, double radj)
+{
+  //called outside of compute(), do not assume correct geometry defined in contact
+  return radi + radj;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormal::calculate_area()
+{
+  return sqrt(gm->dR);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormal::set_fncrit()
+{
+  Fncrit = fabs(gm->Fntot);
+}
+
+/* ----------------------------------------------------------------------
+   No model
+------------------------------------------------------------------------- */
+
+GranSubModNormalNone::GranSubModNormalNone(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalNone::calculate_forces()
+{
+  return 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   Hookean normal force
+------------------------------------------------------------------------- */
+
+GranSubModNormalHooke::GranSubModNormalHooke(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
+{
+  num_coeffs = 2;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalHooke::coeffs_to_local()
+{
+  k = coeffs[0];
+  damp = coeffs[1];
+
+  if (k < 0.0 || damp < 0.0) error->all(FLERR, "Illegal Hooke normal model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalHooke::calculate_forces()
+{
+  return k * gm->delta;
+}
+
+/* ----------------------------------------------------------------------
+   Hertzian normal force
+------------------------------------------------------------------------- */
+
+GranSubModNormalHertz::GranSubModNormalHertz(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
+{
+  num_coeffs = 2;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalHertz::coeffs_to_local()
+{
+  k = coeffs[0];
+  damp = coeffs[1];
+
+  if (k < 0.0 || damp < 0.0) error->all(FLERR, "Illegal Hertz normal model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalHertz::calculate_forces()
+{
+  return k * gm->area * gm->delta;
+}
+
+/* ----------------------------------------------------------------------
+   Hertzian normal force with material properties
+------------------------------------------------------------------------- */
+
+GranSubModNormalHertzMaterial::GranSubModNormalHertzMaterial(GranularModel *gm, LAMMPS *lmp) : GranSubModNormalHertz(gm, lmp)
+{
+  material_properties = 1;
+  num_coeffs = 3;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalHertzMaterial::coeffs_to_local()
+{
+  Emod = coeffs[0];
+  damp = coeffs[1];
+  poiss = coeffs[2];
+  if (gm->contact_type == PAIR) {
+    k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
+  } else {
+    k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+  }
+
+  if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal Hertz material normal model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalHertzMaterial::mix_coeffs(double* icoeffs, double* jcoeffs)
+{
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
+  coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
+  coeffs_to_local();
+}
+
+/* ----------------------------------------------------------------------
+   DMT normal force
+------------------------------------------------------------------------- */
+
+GranSubModNormalDMT::GranSubModNormalDMT(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
+{
+  material_properties = 1;
+  cohesive_flag = 1;
+  num_coeffs = 4;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalDMT::coeffs_to_local()
+{
+  Emod = coeffs[0];
+  damp = coeffs[1];
+  poiss = coeffs[2];
+  cohesion = coeffs[3];
+  if (gm->contact_type == PAIR) {
+    k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
+  } else {
+    k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+  }
+
+  if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal DMT normal model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalDMT::mix_coeffs(double* icoeffs, double* jcoeffs)
+{
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
+  coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
+  coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
+  coeffs_to_local();
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalDMT::calculate_forces()
+{
+  Fne = k * gm->area * gm->delta;
+  F_pulloff = 4.0 * MathConst::MY_PI * cohesion * gm->Reff;
+  Fne -= F_pulloff;
+  return Fne;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalDMT::set_fncrit()
+{
+  Fncrit = fabs(Fne + 2.0 * F_pulloff);
+}
+
+/* ----------------------------------------------------------------------
+   JKR normal force
+------------------------------------------------------------------------- */
+
+GranSubModNormalJKR::GranSubModNormalJKR(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
+{
+  material_properties = 1;
+  cohesive_flag = 1;
+  beyond_contact = 1;
+  num_coeffs = 4;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalJKR::coeffs_to_local()
+{
+  Emod = coeffs[0];
+  damp = coeffs[1];
+  poiss = coeffs[2];
+  cohesion = coeffs[3];
+
+  if (gm->contact_type == PAIR) {
+    Emix = mix_stiffnessE(Emod, Emod, poiss, poiss);
+  } else {
+    Emix = mix_stiffnessE_wall(Emod, poiss);
+  }
+
+  k = FOURTHIRDS * Emix;
+
+  if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal JKR normal model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalJKR::mix_coeffs(double* icoeffs, double* jcoeffs)
+{
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
+  coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
+  coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
+  coeffs_to_local();
+}
+
+/* ---------------------------------------------------------------------- */
+
+bool GranSubModNormalJKR::touch()
+{
+  double area_at_pulloff, R2, delta_pulloff, dist_pulloff;
+  bool touchflag;
+
+  if (gm->touch) {
+    R2 = gm->Reff * gm->Reff;
+    area_at_pulloff = cbrt(9.0 * MY_PI * cohesion * R2 / (4.0 * Emix));
+    delta_pulloff = area_at_pulloff * area_at_pulloff / gm->Reff - 2.0 * sqrt(MY_PI * cohesion * area_at_pulloff / Emix);
+    dist_pulloff = gm->radsum - delta_pulloff;
+    touchflag = gm->rsq < (dist_pulloff * dist_pulloff);
+  } else {
+    touchflag = gm->rsq < (gm->radsum * gm->radsum);
+  }
+
+  return touchflag;
+}
+
+/* ----------------------------------------------------------------------
+  called outside of compute(), do not assume geometry defined in contact
+------------------------------------------------------------------------- */
+
+double GranSubModNormalJKR::pulloff_distance(double radi, double radj)
+{
+  double area_at_pulloff, Reff_tmp;
+
+  Reff_tmp = radi * radj / (radi + radj); // May not be defined
+  if (Reff_tmp <= 0) return 0;
+
+  area_at_pulloff = cbrt(9.0 * MY_PI * cohesion * Reff_tmp * Reff_tmp / (4.0 * Emix));
+  return area_at_pulloff * area_at_pulloff / Reff_tmp - 2.0 * sqrt(MY_PI * cohesion * area_at_pulloff / Emix);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalJKR::calculate_area()
+{
+  double R2, dR2, t0, t1, t2, t3, t4, t5, t6;
+  double sqrt1, sqrt2, sqrt3;
+
+  R2 = gm->Reff * gm->Reff;
+  dR2 = gm->dR * gm->dR;
+  t0 = cohesion * cohesion * R2 * R2 * Emix;
+  t1 = PI27SQ * t0;
+  t2 = 8.0 * gm->dR * dR2 * Emix * Emix * Emix;
+  t3 = 4.0 * dR2 * Emix;
+
+  // in case sqrt(0) < 0 due to precision issues
+  sqrt1 = MAX(0, t0 * (t1 + 2.0 * t2));
+  t4 = cbrt(t1 + t2 + THREEROOT3 * MY_PI * sqrt(sqrt1));
+  t5 = t3 / t4 + t4 / Emix;
+  sqrt2 = MAX(0, 2.0 * gm->dR + t5);
+  t6 = sqrt(sqrt2);
+  sqrt3 = MAX(0, 4.0 * gm->dR - t5 + SIXROOT6 * cohesion * MY_PI * R2 / (Emix * t6));
+
+  return INVROOT6 * (t6 + sqrt(sqrt3));
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModNormalJKR::calculate_forces()
+{
+  double a2;
+  a2 = gm->area * gm->area;
+  Fne = k * gm->area * a2 / gm->Reff - MY_2PI * a2 * sqrt(4.0 * cohesion * Emix / (MY_PI * gm->area));
+  F_pulloff = 3.0 * MY_PI * cohesion * gm->Reff;
+
+  return Fne;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModNormalJKR::set_fncrit()
+{
+  Fncrit = fabs(Fne + 2.0 * F_pulloff);
+}

src/GRANULAR/gran_sub_mod_normal.h

@@ -0,0 +1,139 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModNormalNone,
+         NORMAL);
+
+GranSubModStyle(hooke,
+         GranSubModNormalHooke,
+         NORMAL);
+
+GranSubModStyle(hertz,
+         GranSubModNormalHertz,
+         NORMAL);
+
+GranSubModStyle(hertz/material,
+         GranSubModNormalHertzMaterial,
+         NORMAL);
+
+GranSubModStyle(dmt,
+         GranSubModNormalDMT,
+         NORMAL);
+
+GranSubModStyle(jkr,
+         GranSubModNormalJKR,
+         NORMAL);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_NORMAL_H
+#define GRAN_SUB_MOD_NORMAL_H
+
+#include "gran_sub_mod.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModNormal : public GranSubMod {
+ public:
+  GranSubModNormal(class GranularModel *, class LAMMPS *);
+  ~GranSubModNormal() {};
+  virtual bool touch();
+  virtual double pulloff_distance(double, double);
+  virtual double calculate_area();
+  virtual double calculate_forces() = 0;
+  virtual void set_fncrit();
+  double damp; // argument historically needed by damping
+  double Emod, poiss;
+  double Fncrit;
+  int material_properties, cohesive_flag;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalNone : public GranSubModNormal {
+ public:
+  GranSubModNormalNone(class GranularModel *, class LAMMPS *);
+  double calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalHooke : public GranSubModNormal {
+ public:
+  GranSubModNormalHooke(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  double calculate_forces();
+ protected:
+  double k;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalHertz : public GranSubModNormal {
+ public:
+  GranSubModNormalHertz(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  double calculate_forces();
+ protected:
+  double k;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalHertzMaterial : public GranSubModNormalHertz {
+ public:
+  GranSubModNormalHertzMaterial(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void mix_coeffs(double*, double*) override;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalDMT : public GranSubModNormal {
+ public:
+  GranSubModNormalDMT(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void mix_coeffs(double*, double*) override;
+  double calculate_forces();
+  void set_fncrit() override;
+ protected:
+  double k, cohesion;
+  double F_pulloff, Fne;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModNormalJKR : public GranSubModNormal {
+ public:
+  GranSubModNormalJKR(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void mix_coeffs(double*, double*) override;
+  bool touch() override;
+  double pulloff_distance(double, double) override;
+  double calculate_area() override;
+  double calculate_forces();
+  void set_fncrit() override;
+ protected:
+  double k, cohesion;
+  double Emix, F_pulloff, Fne;
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_NORMAL_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/gran_sub_mod_rolling.cpp

@@ -0,0 +1,124 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_normal.h"
+#include "gran_sub_mod_rolling.h"
+#include "granular_model.h"
+#include "error.h"
+#include "math_const.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathConst;
+using namespace MathExtra;
+
+#define EPSILON 1e-10
+
+/* ----------------------------------------------------------------------
+   Default rolling friction model
+------------------------------------------------------------------------- */
+
+GranSubModRolling::GranSubModRolling(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   No model
+------------------------------------------------------------------------- */
+
+GranSubModRollingNone::GranSubModRollingNone(GranularModel *gm, LAMMPS *lmp) : GranSubModRolling(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   SDS rolling friction model
+------------------------------------------------------------------------- */
+
+GranSubModRollingSDS::GranSubModRollingSDS(GranularModel *gm, LAMMPS *lmp) : GranSubModRolling(gm, lmp)
+{
+  num_coeffs = 3;
+  size_history = 3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModRollingSDS::coeffs_to_local()
+{
+  k = coeffs[0];
+  gamma = coeffs[1];
+  mu = coeffs[2];
+
+  if (k < 0.0 || mu < 0.0 || gamma < 0.0)
+    error->all(FLERR, "Illegal SDS rolling model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModRollingSDS::calculate_forces()
+{
+  int rhist0, rhist1, rhist2, frameupdate;
+  double Frcrit, rolldotn, rollmag, prjmag, magfr, hist_temp[3], scalefac, temp_array[3];
+  double k_inv, magfr_inv;
+
+  rhist0 = history_index;
+  rhist1 = rhist0 + 1;
+  rhist2 = rhist1 + 1;
+
+  Frcrit = mu * gm->normal_model->Fncrit;
+
+  if (gm->history_update) {
+    hist_temp[0] = gm->history[rhist0];
+    hist_temp[1] = gm->history[rhist1];
+    hist_temp[2] = gm->history[rhist2];
+    rolldotn = dot3(hist_temp, gm->nx);
+
+    frameupdate = (fabs(rolldotn) * k)  > (EPSILON * Frcrit);
+    if (frameupdate) { // rotate into tangential plane
+      rollmag = len3(hist_temp);
+      // projection
+      scale3(rolldotn, gm->nx, temp_array);
+      sub3(hist_temp, temp_array, hist_temp);
+
+      // also rescale to preserve magnitude
+      prjmag = len3(hist_temp);
+      if (prjmag > 0) scalefac = rollmag / prjmag;
+      else scalefac = 0;
+      scale3(scalefac, hist_temp);
+    }
+    scale3(gm->dt, gm->vrl, temp_array);
+    add3(hist_temp, temp_array, hist_temp);
+  }
+
+  scaleadd3(-k, hist_temp, -gamma, gm->vrl, gm->fr);
+
+  // rescale frictional displacements and forces if needed
+  magfr = len3(gm->fr);
+  if (magfr > Frcrit) {
+    rollmag = len3(hist_temp);
+    if (rollmag != 0.0) {
+      k_inv = 1.0 / k;
+      magfr_inv = 1.0 / magfr;
+      scale3(-Frcrit * k_inv * magfr_inv, gm->fr, hist_temp);
+      scale3(-gamma * k_inv, gm->vrl, temp_array);
+      add3(hist_temp, temp_array, hist_temp);
+
+      scale3(Frcrit * magfr_inv, gm->fr);
+    } else {
+      zero3(gm->fr);
+    }
+  }
+
+  if (gm->history_update) {
+    gm->history[rhist0] = hist_temp[0];
+    gm->history[rhist1] = hist_temp[1];
+    gm->history[rhist2] = hist_temp[2];
+  }
+}

src/GRANULAR/gran_sub_mod_rolling.h

@@ -0,0 +1,64 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModRollingNone,
+         ROLLING);
+
+GranSubModStyle(sds,
+         GranSubModRollingSDS,
+         ROLLING);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_ROLLING_H
+#define GRAN_SUB_MOD_ROLLING_H
+
+#include "gran_sub_mod.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModRolling : public GranSubMod {
+ public:
+  GranSubModRolling(class GranularModel *, class LAMMPS *);
+  ~GranSubModRolling() {};
+  virtual void calculate_forces() = 0;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModRollingNone : public GranSubModRolling {
+ public:
+  GranSubModRollingNone(class GranularModel *, class LAMMPS *);
+  void calculate_forces() {};
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModRollingSDS : public GranSubModRolling {
+ public:
+  GranSubModRollingSDS(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void calculate_forces();
+ protected:
+  double k, mu, gamma;
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_ROLLING_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/gran_sub_mod_tangential.cpp

@@ -0,0 +1,404 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_damping.h"
+#include "gran_sub_mod_normal.h"
+#include "gran_sub_mod_tangential.h"
+#include "granular_model.h"
+#include "error.h"
+#include "math_const.h"
+#include "math_extra.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathConst;
+using namespace MathExtra;
+
+#define EPSILON 1e-10
+
+/* ----------------------------------------------------------------------
+   Default model
+------------------------------------------------------------------------- */
+
+GranSubModTangential::GranSubModTangential(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   No model
+------------------------------------------------------------------------- */
+
+GranSubModTangentialNone::GranSubModTangentialNone(GranularModel *gm, LAMMPS *lmp) : GranSubModTangential(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   Linear model with no history
+------------------------------------------------------------------------- */
+
+GranSubModTangentialLinearNoHistory::GranSubModTangentialLinearNoHistory(GranularModel *gm, LAMMPS *lmp) : GranSubModTangential(gm, lmp)
+{
+  num_coeffs = 2;
+  size_history = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialLinearNoHistory::coeffs_to_local()
+{
+  k = 0.0; // No tangential stiffness with no history
+  xt = coeffs[0];
+  mu = coeffs[1];
+
+  if (k < 0.0 || xt < 0.0 || mu < 0.0)
+    error->all(FLERR, "Illegal linear no history tangential model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialLinearNoHistory::calculate_forces()
+{
+  // classic pair gran/hooke (no history)
+  damp = xt * gm->damping_model->damp_prefactor;
+
+  double Fscrit = mu * gm->normal_model->Fncrit;
+  double fsmag = damp * gm->vrel;
+
+  double Ft;
+  if (gm->vrel != 0.0) Ft = MIN(Fscrit, fsmag) / gm->vrel;
+  else Ft = 0.0;
+
+  scale3(-Ft, gm->vtr, gm->fs);
+}
+
+/* ----------------------------------------------------------------------
+   Linear model with history
+------------------------------------------------------------------------- */
+
+GranSubModTangentialLinearHistory::GranSubModTangentialLinearHistory(GranularModel *gm, LAMMPS *lmp) : GranSubModTangential(gm, lmp)
+{
+  num_coeffs = 3;
+  size_history = 3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialLinearHistory::coeffs_to_local()
+{
+  k = coeffs[0];
+  xt = coeffs[1];
+  mu = coeffs[2];
+
+  if (k < 0.0 || xt < 0.0 || mu < 0.0)
+    error->all(FLERR, "Illegal linear tangential model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialLinearHistory::calculate_forces()
+{
+  // Note: this is the same as the base Mindlin calculation except k isn't scaled by area
+  double magfs, magfs_inv, rsht, shrmag, prjmag, temp_dbl, temp_array[3];
+  int frame_update = 0;
+
+  damp = xt * gm->damping_model->damp_prefactor;
+
+  double Fscrit = gm->normal_model->Fncrit * mu;
+  double *history = & gm->history[history_index];
+
+  // rotate and update displacements / force.
+  // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235
+  if (gm->history_update) {
+    rsht = dot3(history, gm->nx);
+    frame_update = (fabs(rsht) * k) > (EPSILON * Fscrit);
+
+    if (frame_update) {
+      shrmag = len3(history);
+
+      // projection
+      scale3(rsht, gm->nx, temp_array);
+      sub3(history, temp_array, history);
+
+      // also rescale to preserve magnitude
+      prjmag = len3(history);
+      if (prjmag > 0) temp_dbl = shrmag / prjmag;
+      else temp_dbl = 0;
+      scale3(temp_dbl, history);
+    }
+
+    // update history, tangential force
+    // see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46
+    scale3(gm->dt, gm->vtr, temp_array);
+    add3(history, temp_array, history);
+  }
+
+  // tangential forces = history + tangential velocity damping
+  scale3(-k, history, gm->fs);
+  scale3(damp, gm->vtr, temp_array);
+  sub3(gm->fs, temp_array, gm->fs);
+
+  // rescale frictional displacements and forces if needed
+  magfs = len3(gm->fs);
+  if (magfs > Fscrit) {
+    shrmag = len3(history);
+    if (shrmag != 0.0) {
+      magfs_inv = 1.0 / magfs;
+      scale3(Fscrit * magfs_inv, gm->fs, history);
+      scale3(damp, gm->vtr, temp_array);
+      add3(history, temp_array, history);
+      scale3(-1.0 / k, history);
+      scale3(Fscrit * magfs_inv, gm->fs);
+    } else {
+      zero3(gm->fs);
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Linear model with history from pair gran/hooke/history
+------------------------------------------------------------------------- */
+
+GranSubModTangentialLinearHistoryClassic::GranSubModTangentialLinearHistoryClassic(GranularModel *gm, LAMMPS *lmp) : GranSubModTangentialLinearHistory(gm, lmp)
+{
+  area_flag = 1; // Sets gran/hooke/history behavior
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialLinearHistoryClassic::calculate_forces()
+{
+  double magfs, magfs_inv, rsht, shrmag;
+  double temp_array[3];
+
+  damp = xt * gm->damping_model->damp_prefactor;
+
+  double Fscrit = gm->normal_model->Fncrit * mu;
+  double *history = & gm->history[history_index];
+
+  // update history
+  if (gm->history_update) {
+    scale3(gm->dt, gm->vtr, temp_array);
+    add3(history, temp_array, history);
+  }
+
+  shrmag = len3(history);
+
+  // rotate shear displacements
+  if (gm->history_update) {
+    rsht = dot3(history, gm->nx);
+    scale3(rsht, gm->nx, temp_array);
+    sub3(history, temp_array, history);
+  }
+
+  // tangential forces = history + tangential velocity damping
+  if (area_flag) scale3(-k * gm->area, history, gm->fs);
+  else scale3(-k, history, gm->fs);
+  scale3(damp, gm->vtr, temp_array);
+  sub3(gm->fs, temp_array, gm->fs);
+
+  // rescale frictional displacements and forces if needed
+  magfs = len3(gm->fs);
+  if (magfs > Fscrit) {
+    if (shrmag != 0.0) {
+      magfs_inv = 1.0 / magfs;
+      scale3(Fscrit * magfs_inv, gm->fs, history);
+      scale3(damp, gm->vtr, temp_array);
+      add3(history, temp_array, history);
+      scale3(-1.0 / k, history);
+      scale3(Fscrit * magfs_inv, gm->fs);
+    } else {
+      zero3(gm->fs);
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Mindlin from pair gran/hertz/history
+------------------------------------------------------------------------- */
+
+GranSubModTangentialMindlinClassic::GranSubModTangentialMindlinClassic(GranularModel *gm, LAMMPS *lmp) : GranSubModTangentialLinearHistoryClassic(gm, lmp)
+{
+  area_flag = 1; // Sets gran/hertz/history behavior
+}
+
+/* ----------------------------------------------------------------------
+   Mindlin model
+------------------------------------------------------------------------- */
+
+GranSubModTangentialMindlin::GranSubModTangentialMindlin(GranularModel *gm, LAMMPS *lmp) : GranSubModTangential(gm, lmp)
+{
+  num_coeffs = 3;
+  size_history = 3;
+  mindlin_force = 0;
+  mindlin_rescale = 0;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialMindlin::coeffs_to_local()
+{
+  k = coeffs[0];
+  xt = coeffs[1];
+  mu = coeffs[2];
+
+  if (k == -1) {
+    if (!gm->normal_model->material_properties)
+      error->all(FLERR, "Must either specify tangential stiffness or material properties for normal model for the Mindlin tangential style");
+
+    double Emod = gm->normal_model->Emod;
+    double poiss = gm->normal_model->poiss;
+
+    if (gm->contact_type == PAIR) {
+      k = 8.0 * mix_stiffnessG(Emod, Emod, poiss, poiss);
+    } else {
+      k = 8.0 * mix_stiffnessG_wall(Emod, poiss);
+    }
+  }
+
+  if (k < 0.0 || xt < 0.0 || mu < 0.0)
+    error->all(FLERR, "Illegal Mindlin tangential model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialMindlin::mix_coeffs(double* icoeffs, double* jcoeffs)
+{
+  if (icoeffs[0] == -1 || jcoeffs[0] == -1) coeffs[0] = -1;
+  else coeffs[0] = mix_geom(icoeffs[0], jcoeffs[0]);
+  coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
+  coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
+  coeffs_to_local();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTangentialMindlin::calculate_forces()
+{
+  double k_scaled, magfs, magfs_inv, rsht, shrmag, prjmag, temp_dbl;
+  double temp_array[3];
+  int frame_update = 0;
+
+  damp = xt * gm->damping_model->damp_prefactor;
+
+  double *history = & gm->history[history_index];
+  double Fscrit = gm->normal_model->Fncrit * mu;
+
+  k_scaled = k * gm->area;
+
+  // on unloading, rescale the shear displacements/force
+  if (mindlin_rescale)
+    if (gm->area < history[3])
+      scale3(gm->area / history[3], history);
+
+  // rotate and update displacements / force.
+  // see e.g. eq. 17 of Luding, Gran. Matter 2008, v10,p235
+  if (gm->history_update) {
+    rsht = dot3(history, gm->nx);
+    if (mindlin_force) {
+      frame_update = fabs(rsht) > (EPSILON * Fscrit);
+    } else {
+      frame_update = (fabs(rsht) * k_scaled) > (EPSILON * Fscrit);
+    }
+
+    if (frame_update) {
+      shrmag = len3(history);
+      // projection
+      scale3(rsht, gm->nx, temp_array);
+      sub3(history, temp_array, history);
+      // also rescale to preserve magnitude
+      prjmag = len3(history);
+      if (prjmag > 0) temp_dbl = shrmag / prjmag;
+      else temp_dbl = 0;
+      scale3(temp_dbl, history);
+    }
+
+    // update history
+    if (mindlin_force) {
+      // tangential force
+      // see e.g. eq. 18 of Thornton et al, Pow. Tech. 2013, v223,p30-46
+      scale3(-k_scaled * gm->dt, gm->vtr, temp_array);
+    } else {
+      scale3(gm->dt, gm->vtr, temp_array);
+    }
+    add3(history, temp_array, history);
+
+    if (mindlin_rescale) history[3] = gm->area;
+  }
+
+  // tangential forces = history + tangential velocity damping
+  scale3(-damp, gm->vtr, gm->fs);
+
+  if (!mindlin_force) {
+    scale3(k_scaled, history, temp_array);
+    sub3(gm->fs, temp_array, gm->fs);
+  } else {
+    add3(gm->fs, history, gm->fs);
+  }
+
+  // rescale frictional displacements and forces if needed
+  magfs = len3(gm->fs);
+  if (magfs > Fscrit) {
+    shrmag = len3(history);
+    if (shrmag != 0.0) {
+      magfs_inv = 1.0 / magfs;
+      scale3(Fscrit * magfs_inv, gm->fs, history);
+      scale3(damp, gm->vtr, temp_array);
+      add3(history, temp_array, history);
+
+      if (!mindlin_force)
+        scale3(-1.0 / k_scaled, history);
+
+      scale3(Fscrit * magfs_inv, gm->fs);
+    } else {
+      zero3(gm->fs);
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Mindlin force model
+------------------------------------------------------------------------- */
+
+GranSubModTangentialMindlinForce::GranSubModTangentialMindlinForce(GranularModel *gm, LAMMPS *lmp) : GranSubModTangentialMindlin(gm, lmp)
+{
+  mindlin_force = 1;
+}
+
+/* ----------------------------------------------------------------------
+   Mindlin rescale model
+------------------------------------------------------------------------- */
+
+GranSubModTangentialMindlinRescale::GranSubModTangentialMindlinRescale(GranularModel *gm, LAMMPS *lmp) : GranSubModTangentialMindlin(gm, lmp)
+{
+  size_history = 4;
+  mindlin_rescale = 1;
+
+  nondefault_history_transfer = 1;
+  transfer_history_factor = new double[size_history];
+  for (int i = 0; i < size_history; i++) transfer_history_factor[i] = -1.0;
+  transfer_history_factor[3] = +1;
+}
+
+/* ----------------------------------------------------------------------
+   Mindlin rescale force model
+------------------------------------------------------------------------- */
+
+GranSubModTangentialMindlinRescaleForce::GranSubModTangentialMindlinRescaleForce(GranularModel *gm, LAMMPS *lmp) : GranSubModTangentialMindlin(gm, lmp)
+{
+  size_history = 4;
+  mindlin_force = 1;
+  mindlin_rescale = 1;
+
+  nondefault_history_transfer = 1;
+  transfer_history_factor = new double[size_history];
+  for (int i = 0; i < size_history; i++) transfer_history_factor[i] = -1.0;
+  transfer_history_factor[3] = +1;
+}

src/GRANULAR/gran_sub_mod_tangential.h

@@ -0,0 +1,153 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModTangentialNone,
+         TANGENTIAL);
+
+GranSubModStyle(linear_nohistory,
+         GranSubModTangentialLinearNoHistory,
+         TANGENTIAL);
+
+GranSubModStyle(linear_history,
+         GranSubModTangentialLinearHistory,
+         TANGENTIAL);
+
+GranSubModStyle(linear_history_classic,
+         GranSubModTangentialLinearHistoryClassic,
+         TANGENTIAL);
+
+GranSubModStyle(mindlin_classic,
+         GranSubModTangentialMindlinClassic,
+         TANGENTIAL);
+
+GranSubModStyle(mindlin,
+         GranSubModTangentialMindlin,
+         TANGENTIAL);
+
+GranSubModStyle(mindlin/force,
+         GranSubModTangentialMindlinForce,
+         TANGENTIAL);
+
+GranSubModStyle(mindlin_rescale,
+         GranSubModTangentialMindlinRescale,
+         TANGENTIAL);
+
+GranSubModStyle(mindlin_rescale/force,
+         GranSubModTangentialMindlinRescaleForce,
+         TANGENTIAL);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_TANGENTIAL_H
+#define GRAN_SUB_MOD_TANGENTIAL_H
+
+#include "gran_sub_mod.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModTangential : public GranSubMod {
+ public:
+  GranSubModTangential(class GranularModel *, class LAMMPS *);
+  virtual ~GranSubModTangential() {};
+  virtual void calculate_forces() = 0;
+  double k, damp, mu; // Used by Marshall twisting model
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialNone : public GranSubModTangential {
+ public:
+  GranSubModTangentialNone(class GranularModel *, class LAMMPS *);
+  void calculate_forces() {};
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialLinearNoHistory : public GranSubModTangential {
+ public:
+  GranSubModTangentialLinearNoHistory(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void calculate_forces();
+ protected:
+  double xt;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialLinearHistory : public GranSubModTangential {
+ public:
+  GranSubModTangentialLinearHistory(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void calculate_forces();
+ protected:
+  double xt;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialLinearHistoryClassic : public GranSubModTangentialLinearHistory {
+ public:
+  GranSubModTangentialLinearHistoryClassic(class GranularModel *, class LAMMPS *);
+  void calculate_forces();
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialMindlinClassic : public GranSubModTangentialLinearHistoryClassic {
+ public:
+  GranSubModTangentialMindlinClassic(class GranularModel *, class LAMMPS *);
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialMindlin : public GranSubModTangential {
+ public:
+  GranSubModTangentialMindlin(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void mix_coeffs(double*, double*) override;
+  void calculate_forces();
+ protected:
+  int mindlin_rescale, mindlin_force;
+  double xt;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialMindlinForce : public GranSubModTangentialMindlin {
+ public:
+  GranSubModTangentialMindlinForce(class GranularModel *, class LAMMPS *);
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialMindlinRescale : public GranSubModTangentialMindlin {
+ public:
+  GranSubModTangentialMindlinRescale(class GranularModel *, class LAMMPS *);
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTangentialMindlinRescaleForce : public GranSubModTangentialMindlin {
+ public:
+  GranSubModTangentialMindlinRescaleForce(class GranularModel *, class LAMMPS *);
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_TANGENTIAL_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/gran_sub_mod_twisting.cpp

@@ -0,0 +1,126 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#include "gran_sub_mod_normal.h"
+#include "gran_sub_mod_tangential.h"
+#include "gran_sub_mod_twisting.h"
+#include "granular_model.h"
+#include "error.h"
+#include "math_const.h"
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathConst;
+
+/* ----------------------------------------------------------------------
+   Default twisting model
+------------------------------------------------------------------------- */
+
+GranSubModTwisting::GranSubModTwisting(GranularModel *gm, LAMMPS *lmp) : GranSubMod(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   No model
+------------------------------------------------------------------------- */
+
+GranSubModTwistingNone::GranSubModTwistingNone(GranularModel *gm, LAMMPS *lmp) : GranSubModTwisting(gm, lmp) {}
+
+/* ----------------------------------------------------------------------
+   Marshall twisting model
+------------------------------------------------------------------------- */
+
+GranSubModTwistingMarshall::GranSubModTwistingMarshall(GranularModel *gm, LAMMPS *lmp) : GranSubModTwisting(gm, lmp)
+{
+  num_coeffs = 0;
+  size_history = 3;
+  area_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+
+void GranSubModTwistingMarshall::init()
+{
+  k_tang = gm->tangential_model->k;
+  mu_tang = gm->tangential_model->mu;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTwistingMarshall::calculate_forces()
+{
+  double signtwist, Mtcrit;
+
+  // Calculate twist coefficients from tangential model & contact geometry
+  // eq 32 of Marshall paper
+  double k = 0.5 * k_tang * gm->area * gm->area;
+  double damp = 0.5 * gm->tangential_model->damp * gm->area * gm->area;
+  double mu = TWOTHIRDS * mu_tang * gm->area;
+
+  if (gm->history_update) {
+    gm->history[history_index] += gm->magtwist * gm->dt;
+  }
+
+  // M_t torque (eq 30)
+  gm->magtortwist = -k * gm->history[history_index] - damp * gm->magtwist;
+  signtwist = (gm->magtwist > 0) - (gm->magtwist < 0);
+  Mtcrit = mu * gm->normal_model->Fncrit; // critical torque (eq 44)
+
+  if (fabs(gm->magtortwist) > Mtcrit) {
+    gm->history[history_index] = (Mtcrit * signtwist - damp * gm->magtwist) / k;
+    gm->magtortwist = -Mtcrit * signtwist; // eq 34
+  }
+}
+
+/* ----------------------------------------------------------------------
+   SDS twisting model
+------------------------------------------------------------------------- */
+
+GranSubModTwistingSDS::GranSubModTwistingSDS(GranularModel *gm, LAMMPS *lmp) : GranSubModTwisting(gm, lmp)
+{
+  num_coeffs = 3;
+  size_history = 3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTwistingSDS::coeffs_to_local()
+{
+  k = coeffs[0];
+  damp = coeffs[1];
+  mu = coeffs[2];
+
+  if (k < 0.0 || mu < 0.0 || damp < 0.0)
+    error->all(FLERR, "Illegal SDS twisting model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModTwistingSDS::calculate_forces()
+{
+  double signtwist, Mtcrit;
+
+  if (gm->history_update) {
+    gm->history[history_index] += gm->magtwist * gm->dt;
+  }
+
+  // M_t torque (eq 30)
+  gm->magtortwist = -k * gm->history[history_index] - damp * gm->magtwist;
+  signtwist = (gm->magtwist > 0) - (gm->magtwist < 0);
+  Mtcrit = mu * gm->normal_model->Fncrit; // critical torque (eq 44)
+
+  if (fabs(gm->magtortwist) > Mtcrit) {
+    gm->history[history_index] = (Mtcrit * signtwist - damp * gm->magtwist) / k;
+    gm->magtortwist = -Mtcrit * signtwist; // eq 34
+  }
+}

src/GRANULAR/gran_sub_mod_twisting.h

@@ -0,0 +1,79 @@
+/* -*- 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 GRAN_SUB_MOD_CLASS
+// clang-format off
+GranSubModStyle(none,
+         GranSubModTwistingNone,
+         TWISTING);
+
+GranSubModStyle(marshall,
+         GranSubModTwistingMarshall,
+         TWISTING);
+
+GranSubModStyle(sds,
+         GranSubModTwistingSDS,
+         TWISTING);
+// clang-format on
+#else
+
+#ifndef GRAN_SUB_MOD_TWISTING_H
+#define GRAN_SUB_MOD_TWISTING_H
+
+#include "gran_sub_mod.h"
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+class GranSubModTwisting : public GranSubMod {
+ public:
+  GranSubModTwisting(class GranularModel *, class LAMMPS *);
+  virtual ~GranSubModTwisting() {};
+  virtual void calculate_forces() = 0;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTwistingNone : public GranSubModTwisting {
+ public:
+  GranSubModTwistingNone(class GranularModel *, class LAMMPS *);
+  void calculate_forces() {};
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTwistingMarshall : public GranSubModTwisting {
+ public:
+  GranSubModTwistingMarshall(class GranularModel *, class LAMMPS *);
+  void init() override;
+  void calculate_forces();
+ protected:
+  double k_tang, mu_tang;
+};
+
+/* ---------------------------------------------------------------------- */
+
+class GranSubModTwistingSDS : public GranSubModTwisting {
+ public:
+  GranSubModTwistingSDS(class GranularModel *, class LAMMPS *);
+  void coeffs_to_local() override;
+  void calculate_forces();
+ protected:
+  double k, mu, damp;
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif /*GRAN_SUB_MOD_TWISTING_H */
+#endif /*GRAN_SUB_MOD_CLASS_H */

src/GRANULAR/granular_model.cpp

@@ -0,0 +1,496 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This class contains a series of tools for DEM contacts
+   Multiple models can be defined and used to calculate forces
+   and torques based on contact geometry
+
+   Contributing authors:
+   Dan Bolintineanu (SNL), Joel Clemmer (SNL)
+----------------------------------------------------------------------- */
+
+#include "granular_model.h"
+#include "gran_sub_mod.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "style_gran_sub_mod.h"  // IWYU pragma: keep
+
+#include <cmath>
+
+using namespace LAMMPS_NS;
+using namespace Granular_NS;
+using namespace MathExtra;
+
+/* ----------------------------------------------------------------------
+   one instance per GranSubMod style in style_gran_sub_mod.h
+------------------------------------------------------------------------- */
+
+template <typename T> static GranSubMod *gran_sub_mod_creator(GranularModel *gm, LAMMPS *lmp)
+{
+  return new T(gm, lmp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+GranularModel::GranularModel(LAMMPS *lmp) : Pointers(lmp)
+{
+  limit_damping = 0;
+  beyond_contact = 0;
+  nondefault_history_transfer = 0;
+  classic_model = 0;
+  contact_type = PAIR;
+
+  normal_model = nullptr;
+  damping_model = nullptr;
+  tangential_model = nullptr;
+  rolling_model = nullptr;
+  twisting_model = nullptr;
+  heat_model = nullptr;
+
+  for (int i = 0; i < NSUBMODELS; i++) sub_models[i] = nullptr;
+  transfer_history_factor = nullptr;
+
+  // extract info from GranSubMod classes listed in style_gran_sub_mod.h
+
+  nclass = 0;
+
+#define GRAN_SUB_MOD_CLASS
+#define GranSubModStyle(key,Class,type) nclass++;
+#include "style_gran_sub_mod.h"  // IWYU pragma: keep
+#undef GranSubModStyle
+#undef GRAN_SUB_MOD_CLASS
+
+  gran_sub_mod_class = new GranSubModCreator[nclass];
+  gran_sub_mod_names = new char*[nclass];
+  gran_sub_mod_types = new int[nclass];
+  nclass = 0;
+
+#define GRAN_SUB_MOD_CLASS
+#define GranSubModStyle(key,Class,type) \
+  gran_sub_mod_class[nclass] = &gran_sub_mod_creator<Class>;   \
+  gran_sub_mod_names[nclass] = (char *) #key; \
+  gran_sub_mod_types[nclass++] = type;
+#include "style_gran_sub_mod.h"  // IWYU pragma: keep
+#undef GranSubModStyle
+#undef GRAN_SUB_MOD_CLASS
+}
+
+/* ---------------------------------------------------------------------- */
+
+GranularModel::~GranularModel()
+{
+  delete [] transfer_history_factor;
+  delete [] gran_sub_mod_class;
+  delete [] gran_sub_mod_names;
+  delete [] gran_sub_mod_types;
+
+  for (int i = 0; i < NSUBMODELS; i ++) delete sub_models[i];
+}
+
+/* ---------------------------------------------------------------------- */
+
+int GranularModel::add_sub_model(char **arg, int iarg, int narg, SubModelType model_type)
+{
+  if (iarg >= narg)
+    error->all(FLERR, "Must specify granular sub model name");
+
+  std::string model_name = std::string(arg[iarg++]);
+  construct_sub_model(model_name, model_type);
+
+  int num_coeffs = sub_models[model_type]->num_coeffs;
+  if (iarg + num_coeffs > narg)
+    error->all(FLERR, "Insufficient arguments provided for {} model", model_name);
+
+  for (int i = 0; i < num_coeffs; i++) {
+    // A few parameters (e.g. kt for tangential mindlin) allow null
+    if (strcmp(arg[iarg + i], "NULL") == 0) sub_models[model_type]->coeffs[i] = -1;
+    else sub_models[model_type]->coeffs[i] = utils::numeric(FLERR,arg[iarg + i],false,lmp);
+  }
+
+  sub_models[model_type]->coeffs_to_local();
+
+  return iarg + num_coeffs;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranularModel::construct_sub_model(std::string model_name, SubModelType model_type)
+{
+  int i;
+  for (i = 0; i < nclass; i++) {
+    if (gran_sub_mod_types[i] == model_type) {
+      if (strcmp(gran_sub_mod_names[i], model_name.c_str()) == 0) {
+        GranSubModCreator &gran_sub_mod_creator = gran_sub_mod_class[i];
+        delete sub_models[model_type];
+        sub_models[model_type] = gran_sub_mod_creator(this, lmp);
+        break;
+      }
+    }
+  }
+
+  if (i == nclass)
+    error->all(FLERR, "Illegal model type {}", model_name);
+
+  sub_models[model_type]->name.assign(model_name);
+  sub_models[model_type]->allocate_coeffs();
+
+  // Assign specific sub model pointer
+  if (model_type == NORMAL) normal_model = dynamic_cast<GranSubModNormal *> (sub_models[model_type]);
+  if (model_type == DAMPING) damping_model = dynamic_cast<GranSubModDamping *> (sub_models[model_type]);
+  if (model_type == TANGENTIAL) tangential_model = dynamic_cast<GranSubModTangential *> (sub_models[model_type]);
+  if (model_type == ROLLING) rolling_model = dynamic_cast<GranSubModRolling *> (sub_models[model_type]);
+  if (model_type == TWISTING) twisting_model = dynamic_cast<GranSubModTwisting *> (sub_models[model_type]);
+  if (model_type == HEAT) heat_model = dynamic_cast<GranSubModHeat *> (sub_models[model_type]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int GranularModel::define_classic_model(char **arg, int iarg, int narg)
+{
+  double kn, kt, gamman, gammat, xmu;
+
+  classic_model = 1;
+
+  if (iarg + 6 >= narg)
+    error->all(FLERR,"Insufficient arguments provided for classic gran model command");
+
+  kn = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
+  if (strcmp(arg[iarg + 2],"NULL") == 0) kt = kn * 2.0 / 7.0;
+  else kt = utils::numeric(FLERR,arg[iarg + 2],false,lmp);
+
+  gamman = utils::numeric(FLERR,arg[iarg + 3],false,lmp);
+  if (strcmp(arg[iarg + 4],"NULL") == 0) gammat = 0.5 * gamman;
+  else gammat = utils::numeric(FLERR,arg[iarg + 4],false,lmp);
+
+  xmu = utils::numeric(FLERR,arg[iarg + 5],false,lmp);
+  int dampflag = utils::inumeric(FLERR,arg[iarg + 6],false,lmp);
+  if (dampflag == 0) gammat = 0.0;
+
+  if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
+      xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
+    error->all(FLERR,"Illegal classic gran model command");
+
+  if (strcmp(arg[iarg],"hooke") == 0) {
+    construct_sub_model("hooke", NORMAL);
+    construct_sub_model("linear_nohistory", TANGENTIAL);
+    construct_sub_model("mass_velocity", DAMPING);
+  } else if (strcmp(arg[iarg],"hooke/history") == 0) {
+    construct_sub_model("hooke", NORMAL);
+    construct_sub_model("linear_history_classic", TANGENTIAL);
+    construct_sub_model("mass_velocity", DAMPING);
+  } else if (strcmp(arg[iarg],"hertz/history") == 0) {
+    // convert Kn and Kt from pressure units to force/distance^2 if Hertzian
+    kn /= force->nktv2p;
+    kt /= force->nktv2p;
+    construct_sub_model("hertz", NORMAL);
+    construct_sub_model("mindlin_classic", TANGENTIAL);
+    construct_sub_model("viscoelastic", DAMPING);
+  } else error->all(FLERR,"Invalid classic gran model");
+
+  // ensure additional models are undefined
+  construct_sub_model("none", ROLLING);
+  construct_sub_model("none", TWISTING);
+  construct_sub_model("none", HEAT);
+
+  // manually parse coeffs
+  normal_model->coeffs[0] = kn;
+  normal_model->coeffs[1] = gamman;
+  tangential_model->coeffs[0] = kt;
+  tangential_model->coeffs[1] = gammat / gamman;
+  tangential_model->coeffs[2] = xmu;
+
+  normal_model->coeffs_to_local();
+  tangential_model->coeffs_to_local();
+  damping_model->coeffs_to_local();
+
+  iarg += 7;
+  return iarg;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranularModel::init()
+{
+  for (int i = 0; i < NSUBMODELS; i++)
+    if (!sub_models[i]) construct_sub_model("none", (SubModelType) i);
+
+  // Must have valid normal, damping, and tangential models
+  if (normal_model->name == "none") error->all(FLERR, "Must specify normal granular model");
+  if (damping_model->name == "none") error->all(FLERR, "Must specify damping granular model");
+  if (tangential_model->name == "none") error->all(FLERR, "Must specify tangential granular model");
+
+  // Twisting, rolling, and heat are optional
+  twisting_defined = rolling_defined = heat_defined = 1;
+  if (twisting_model->name == "none") twisting_defined = 0;
+  if (rolling_model->name == "none") rolling_defined = 0;
+  if (heat_model->name == "none") heat_defined = 0;
+
+  int size_cumulative;
+  size_history = 0;
+  area_flag = 0;
+  for (int i = 0; i < NSUBMODELS; i++) {
+    if (sub_models[i]->nondefault_history_transfer)
+      nondefault_history_transfer = 1;
+    if (sub_models[i]->beyond_contact)
+      beyond_contact = 1;
+    size_history += sub_models[i]->size_history;
+    if (!sub_models[i]->allow_cohesion && normal_model->cohesive_flag)
+      error->all(FLERR,"Cannot use {} model with a cohesive normal model, {}",
+                 sub_models[i]->name, normal_model->name);
+    if (sub_models[i]->area_flag) area_flag = 1;
+  }
+
+  if (limit_damping && normal_model->cohesive_flag)
+    error->all(FLERR,"Cannot limit damping with a cohesive normal model, {}", normal_model->name);
+
+  if (nondefault_history_transfer) {
+    transfer_history_factor = new double[size_history];
+
+    int j;
+    for (int i = 0; i < size_history; i++) {
+      // Find which sub model owns this history value
+      size_cumulative = 0;
+      for (j = 0; j < NSUBMODELS; j++) {
+        if ((size_cumulative + sub_models[j]->size_history) > i) break;
+        size_cumulative += sub_models[j]->size_history;
+      }
+
+      // Check if sub model has nondefault transfers, if so copy its array
+      transfer_history_factor[i] = -1;
+      if (j != NSUBMODELS) {
+        if (sub_models[j]->nondefault_history_transfer) {
+          transfer_history_factor[i] = sub_models[j]->transfer_history_factor[i - size_cumulative];
+        }
+      }
+    }
+  }
+
+  for (int i = 0; i < NSUBMODELS; i++) sub_models[i]->init();
+}
+
+/* ---------------------------------------------------------------------- */
+
+int GranularModel::mix_coeffs(GranularModel *g1, GranularModel *g2)
+{
+  for (int i = 0; i < NSUBMODELS; i++) {
+    if (g1->sub_models[i]->name != g2->sub_models[i]->name) return i;
+
+    construct_sub_model(g1->sub_models[i]->name, (SubModelType) i);
+    sub_models[i]->mix_coeffs(g1->sub_models[i]->coeffs, g2->sub_models[i]->coeffs);
+  }
+
+  limit_damping = MAX(g1->limit_damping, g2->limit_damping);
+
+  return -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranularModel::write_restart(FILE *fp)
+{
+  int num_char, num_coeffs;
+
+  for (int i = 0; i < NSUBMODELS; i++) {
+    num_char = sub_models[i]->name.length();
+    num_coeffs = sub_models[i]->num_coeffs;
+    fwrite(&num_char, sizeof(int), 1, fp);
+    fwrite(sub_models[i]->name.data(), sizeof(char), num_char, fp);
+    fwrite(&num_coeffs, sizeof(int), 1, fp);
+    fwrite(sub_models[i]->coeffs, sizeof(double), num_coeffs, fp);
+  }
+
+  fwrite(&limit_damping, sizeof(int), 1, fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranularModel::read_restart(FILE *fp)
+{
+  int num_char, num_coeff;
+
+  for (int i = 0; i < NSUBMODELS; i++) {
+    if (comm->me == 0)
+      utils::sfread(FLERR, &num_char, sizeof(int), 1, fp, nullptr, error);
+    MPI_Bcast(&num_char, 1, MPI_INT, 0, world);
+
+    std::string model_name (num_char, ' ');
+    if (comm->me == 0)
+      utils::sfread(FLERR, const_cast<char*>(model_name.data()), sizeof(char),num_char, fp, nullptr, error);
+    MPI_Bcast(const_cast<char*>(model_name.data()), num_char, MPI_CHAR, 0, world);
+    construct_sub_model(model_name, (SubModelType) i);
+
+    if (comm->me == 0)
+      utils::sfread(FLERR, &num_coeff, sizeof(int), 1, fp, nullptr, error);
+    MPI_Bcast(&num_coeff, 1, MPI_INT, 0, world);
+    if (num_coeff != sub_models[i]->num_coeffs)
+      error->all(FLERR, "Invalid granular model written to restart file");
+
+    if (comm->me == 0)
+      utils::sfread(FLERR, sub_models[i]->coeffs, sizeof(double), num_coeff, fp, nullptr, error);
+    MPI_Bcast(sub_models[i]->coeffs, num_coeff, MPI_DOUBLE, 0, world);
+    sub_models[i]->coeffs_to_local();
+  }
+
+  if (comm->me == 0)
+    utils::sfread(FLERR, &limit_damping, sizeof(int), 1, fp, nullptr, error);
+  MPI_Bcast(&limit_damping, 1, MPI_INT, 0, world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+bool GranularModel::check_contact()
+{
+  if (contact_type == WALL) {
+    // Used by fix_wall_gran.cpp
+    //   radj = radius of wall
+    //   dx already provided
+    rsq = lensq3(dx);
+    radsum = radi;
+    if (radj == 0) Reff = radi;
+    else Reff = radi * radj / (radi + radj);
+  } else if (contact_type == WALLREGION) {
+    // Used by fix_wall_gran_region.cpp
+    //   radj = radius of wall
+    //   dx and r already provided
+    rsq = r * r;
+    radsum = radi;
+    if (radj == 0) Reff = radi;
+    else Reff = radi * radj / (radi + radj);
+  } else {
+    sub3(xi, xj, dx);
+    rsq = lensq3(dx);
+    radsum = radi + radj;
+    Reff = radi * radj / radsum;
+  }
+
+  touch = normal_model->touch();
+  return touch;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranularModel::calculate_forces()
+{
+  // Standard geometric quantities
+
+  if (contact_type != WALLREGION) r = sqrt(rsq);
+  rinv = 1.0 / r;
+  delta = radsum - r;
+  dR = delta * Reff;
+  scale3(rinv, dx, nx);
+
+  // relative translational velocity
+  sub3(vi, vj, vr);
+
+  // normal component
+  vnnr = dot3(vr, nx);
+  scale3(vnnr, nx, vn);
+
+  // tangential component
+  sub3(vr, vn, vt);
+
+  // relative rotational velocity
+  scaleadd3(radi, omegai, radj, omegaj, wr);
+
+  // relative tangential velocities
+  double temp[3];
+  cross3(wr, nx, temp);
+  sub3(vt, temp, vtr);
+  vrel = len3(vtr);
+
+  // calculate forces/torques
+  double Fdamp, dist_to_contact;
+  if (area_flag)
+    area = normal_model->calculate_area();
+  Fnormal = normal_model->calculate_forces();
+
+  Fdamp = damping_model->calculate_forces();
+  Fntot = Fnormal + Fdamp;
+  if (limit_damping && Fntot < 0.0) Fntot = 0.0;
+
+  normal_model->set_fncrit(); // Needed for tangential, rolling, twisting
+  tangential_model->calculate_forces();
+
+  // sum normal + tangential contributions
+
+  scale3(Fntot, nx, forces);
+  add3(forces, fs, forces);
+
+  // May need to eventually rethink tris..
+  cross3(nx, fs, torquesi);
+  scale3(-1, torquesi);
+
+  if (contact_type == PAIR) {
+    copy3(torquesi, torquesj);
+
+    // Classic pair styles don't scale, but classic option is currently only used by walls
+    dist_to_contact = radi - 0.5 * delta;
+    scale3(dist_to_contact, torquesi);
+    dist_to_contact = radj - 0.5 * delta;
+    scale3(dist_to_contact, torquesj);
+  } else {
+    scale3(radi, torquesi);
+  }
+
+  // Extra modes
+
+  if (rolling_defined || twisting_defined)
+    sub3(omegai, omegaj, relrot);
+
+  if (rolling_defined) {
+    // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
+    // this is different from the Marshall papers, which use the Bagi/Kuhn formulation
+    // for rolling velocity (see Wang et al for why the latter is wrong)
+    vrl[0] = Reff * (relrot[1] * nx[2] - relrot[2] * nx[1]);
+    vrl[1] = Reff * (relrot[2] * nx[0] - relrot[0] * nx[2]);
+    vrl[2] = Reff * (relrot[0] * nx[1] - relrot[1] * nx[0]);
+
+    rolling_model->calculate_forces();
+
+    double torroll[3];
+    cross3(nx, fr, torroll);
+    scale3(Reff, torroll);
+    add3(torquesi, torroll, torquesi);
+    if (contact_type == PAIR) sub3(torquesj, torroll, torquesj);
+  }
+
+  if (twisting_defined) {
+    // omega_T (eq 29 of Marshall)
+    magtwist = dot3(relrot, nx);
+
+    twisting_model->calculate_forces();
+
+    double tortwist[3];
+    scale3(magtortwist, nx, tortwist);
+    add3(torquesi, tortwist, torquesi);
+    if (contact_type == PAIR) sub3(torquesj, tortwist, torquesj);
+  }
+
+  if (heat_defined) {
+    dq = heat_model->calculate_heat();
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute pull-off distance (beyond contact) for a given radius and atom type
+   use temporary variables since this does not use a specific contact geometry
+------------------------------------------------------------------------- */
+
+double GranularModel::pulloff_distance(double radi, double radj)
+{
+  return normal_model->pulloff_distance(radi, radj);
+}

src/GRANULAR/granular_model.h

@@ -0,0 +1,112 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_GRANULAR_MODEL_H
+#define LMP_GRANULAR_MODEL_H
+
+#include "pointers.h"    // IWYU pragma: export
+
+namespace LAMMPS_NS {
+namespace Granular_NS {
+
+enum SubModelType {
+  NORMAL = 0,
+  DAMPING,
+  TANGENTIAL,
+  ROLLING,
+  TWISTING,
+  HEAT,
+  NSUBMODELS
+};
+
+enum ContactType {
+  PAIR = 0,
+  WALL = 1,
+  WALLREGION = 2
+};
+
+// forward declarations
+class GranSubMod;
+class GranSubModNormal;
+class GranSubModDamping;
+class GranSubModTangential;
+class GranSubModRolling;
+class GranSubModTwisting;
+class GranSubModHeat;
+
+class GranularModel : protected Pointers {
+ public:
+  GranularModel(class LAMMPS *);
+  ~GranularModel();
+  void init();
+  bool check_contact();
+  void calculate_forces();
+  double pulloff_distance(double, double);
+
+  int add_sub_model(char **, int, int, SubModelType);
+  int define_classic_model(char **, int, int);
+  void construct_sub_model(std::string, SubModelType);
+  int mix_coeffs(GranularModel*, GranularModel*);
+
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+
+  // Sub models
+  GranSubModNormal *normal_model;
+  GranSubModDamping *damping_model;
+  GranSubModTangential *tangential_model;
+  GranSubModRolling *rolling_model;
+  GranSubModTwisting *twisting_model;
+  GranSubModHeat *heat_model;
+  GranSubMod *sub_models[NSUBMODELS];
+
+  // Extra options
+  int beyond_contact, limit_damping, history_update;
+  ContactType contact_type;
+
+  // History variables
+  int size_history, nondefault_history_transfer;
+  double *transfer_history_factor;
+  double *history;
+
+  // Contact properties/output
+  double Fnormal, forces[3], torquesi[3], torquesj[3], dq;
+
+  double radi, radj, meff, dt, Ti, Tj, area;
+  double Fntot, magtortwist;
+
+  double *xi, *xj, *vi, *vj, *omegai, *omegaj;
+  double fs[3], fr[3], ft[3];
+
+  double dx[3], nx[3], r, rsq, rinv, Reff, radsum, delta, dR;
+  double vr[3], vn[3], vnnr, vt[3], wr[3], vtr[3], vrl[3], relrot[3], vrel;
+  double magtwist;
+  bool touch;
+
+ protected:
+  int rolling_defined, twisting_defined, heat_defined; // Flag optional sub models
+  int classic_model;                                   // Flag original pair/gran calculations
+  int area_flag;                                       // Flag whether area is needed
+
+  int nclass;
+
+  typedef class GranSubMod *(*GranSubModCreator)(class GranularModel *, class LAMMPS *);
+  GranSubModCreator *gran_sub_mod_class;
+  char **gran_sub_mod_names;
+  int *gran_sub_mod_types;
+};
+
+}    // namespace Granular_NS
+}    // namespace LAMMPS_NS
+
+#endif

src/GRANULAR/pair_granular.h

@@ -21,9 +21,14 @@ PairStyle(granular,PairGranular);
 #define LMP_PAIR_GRANULAR_H
 
 #include "pair.h"
+#include <vector>
 
 namespace LAMMPS_NS {
 
+namespace Granular_NS {
+  class GranularModel;
+}
+
 class PairGranular : public Pair {
  public:
   PairGranular(class LAMMPS *);
@@ -44,7 +49,6 @@ class PairGranular : public Pair {
   double radii2cut(double, double) override;
 
  protected:
-  double dt;
   int freeze_group_bit;
   int use_history;
 
@@ -63,43 +67,21 @@ class PairGranular : public Pair {
   int nmax;                // allocated size of mass_rigid
 
   void allocate();
-  void transfer_history(double *, double *) override;
+  void transfer_history(double *, double *, int, int) override;
+  void prune_models();
 
  private:
   int size_history;
-  int *history_transfer_factors;
+  int heat_flag;
 
-  // model choices
-  int **normal_model, **damping_model;
-  int **tangential_model, **roll_model, **twist_model;
-  int **limit_damping;
-
-  // history flags
-  int normal_history, tangential_history, roll_history, twist_history;
-
-  // indices of history entries
-  int normal_history_index;
-  int tangential_history_index;
-  int roll_history_index;
-  int twist_history_index;
-
-  // per-type material coefficients
-  double **Emod, **poiss, **Gmod;
-
-  // per-type coefficients, set in pair coeff command
-  double ***normal_coeffs;
-  double ***tangential_coeffs;
-  double ***roll_coeffs;
-  double ***twist_coeffs;
+  // granular models
+  int nmodels, maxmodels;
+  class Granular_NS::GranularModel** models_list;
+  int **types_indices;
 
   // optional user-specified global cutoff, per-type user-specified cutoffs
   double **cutoff_type;
   double cutoff_global;
-
-  double mix_stiffnessE(double, double, double, double);
-  double mix_stiffnessG(double, double, double, double);
-  double mix_geom(double, double);
-  double pulloff_distance(double, double, int, int);
 };
 
 }    // namespace LAMMPS_NS

src/MISC/pair_tracker.cpp

@@ -514,7 +514,7 @@ double PairTracker::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, d
    only needed if any history entries i-j are not just negative of j-i entries
 ------------------------------------------------------------------------- */
 
-void PairTracker::transfer_history(double *source, double *target)
+void PairTracker::transfer_history(double *source, double *target, int itype, int jtype)
 {
   for (int i = 0; i < size_history; i++) target[i] = source[i];
 }

src/MISC/pair_tracker.h

@@ -40,7 +40,7 @@ class PairTracker : public Pair {
   double single(int, int, int, int, double, double, double, double &) override;
   double atom2cut(int) override;
   double radii2cut(double, double) override;
-  void transfer_history(double *, double *) override;
+  void transfer_history(double *, double *, int, int) override;
 
  protected:
   int sizeflag;

src/Make.sh

@@ -78,26 +78,27 @@ cmd=$1
 
 if (test $cmd = "style") || (test $cmd = "packages") then
 
-  $cmd ANGLE_CLASS     angle_      angle      force
-  $cmd ATOM_CLASS      atom_vec_   atom       atom      atom_vec_hybrid
-  $cmd BODY_CLASS      body_       body       atom_vec_body
-  $cmd BOND_CLASS      bond_       bond       force
-  $cmd COMMAND_CLASS   ""          command    input
-  $cmd COMPUTE_CLASS   compute_    compute    modify
-  $cmd DIHEDRAL_CLASS  dihedral_   dihedral   force
-  $cmd DUMP_CLASS      dump_       dump       output    write_dump
-  $cmd FIX_CLASS       fix_        fix        modify
-  $cmd IMPROPER_CLASS  improper_   improper   force
-  $cmd INTEGRATE_CLASS ""          integrate  update
-  $cmd KSPACE_CLASS    ""          kspace     force
-  $cmd MINIMIZE_CLASS  min_        minimize   update
-  $cmd NBIN_CLASS      nbin_       nbin       neighbor
-  $cmd NPAIR_CLASS     npair_      npair      neighbor
-  $cmd NSTENCIL_CLASS  nstencil_   nstencil   neighbor
-  $cmd NTOPO_CLASS     ntopo_      ntopo      neighbor
-  $cmd PAIR_CLASS      pair_       pair       force
-  $cmd READER_CLASS    reader_     reader     read_dump
-  $cmd REGION_CLASS    region_     region     domain
+  $cmd ANGLE_CLASS        angle_         angle         force
+  $cmd ATOM_CLASS         atom_vec_      atom          atom      atom_vec_hybrid
+  $cmd BODY_CLASS         body_          body          atom_vec_body
+  $cmd BOND_CLASS         bond_          bond          force
+  $cmd COMMAND_CLASS      ""             command       input
+  $cmd COMPUTE_CLASS      compute_       compute       modify
+  $cmd DIHEDRAL_CLASS     dihedral_      dihedral      force
+  $cmd DUMP_CLASS         dump_          dump          output    write_dump
+  $cmd FIX_CLASS          fix_           fix           modify
+  $cmd GRAN_SUB_MOD_CLASS gran_sub_mod_  gran_sub_mod  granular_model
+  $cmd IMPROPER_CLASS     improper_      improper      force
+  $cmd INTEGRATE_CLASS    ""             integrate     update
+  $cmd KSPACE_CLASS       ""             kspace        force
+  $cmd MINIMIZE_CLASS     min_           minimize      update
+  $cmd NBIN_CLASS         nbin_          nbin          neighbor
+  $cmd NPAIR_CLASS        npair_         npair         neighbor
+  $cmd NSTENCIL_CLASS     nstencil_      nstencil      neighbor
+  $cmd NTOPO_CLASS        ntopo_         ntopo         neighbor
+  $cmd PAIR_CLASS         pair_          pair          force
+  $cmd READER_CLASS       reader_        reader        read_dump
+  $cmd REGION_CLASS       region_        region        domain
 
 # edit Makefile.lib, for creating non-shared lib
 # called by "make makelib"

src/atom.cpp

@@ -125,6 +125,8 @@ Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
   radius = rmass = nullptr;
   ellipsoid = line = tri = body = nullptr;
   quat = nullptr;
+  temperature = nullptr;
+  heatflow = nullptr;
 
   // molecular systems
 
@@ -421,6 +423,9 @@ void Atom::peratom_create()
   add_peratom("tri",&tri,INT,0);
   add_peratom("body",&body,INT,0);
 
+  add_peratom("temperature",&temperature,DOUBLE,0);
+  add_peratom("heatflow",&heatflow,DOUBLE,0);
+
   // BPM package
 
   add_peratom("quat",&quat,DOUBLE,4);
@@ -623,6 +628,7 @@ void Atom::set_atomflag_defaults()
   molecule_flag = molindex_flag = molatom_flag = 0;
   q_flag = mu_flag = 0;
   rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
+  temperature_flag = heatflow_flag = 0;
   vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
   cs_flag = csforce_flag = vforce_flag = ervelforce_flag = etag_flag = 0;
   rho_flag = esph_flag = cv_flag = vest_flag = 0;
@@ -2835,6 +2841,14 @@ length of the data area, and a short description.
      - double
      - 4
      - four quaternion components of the particles
+   * - temperature
+     - double
+     - 1
+     - temperature of the particles
+   * - heatflow
+     - double
+     - 1
+     - heatflow of the particles
    * - i_name
      - int
      - 1
@@ -2891,6 +2905,8 @@ void *Atom::extract(const char *name)
   if (strcmp(name,"tri") == 0) return (void *) tri;
   if (strcmp(name,"body") == 0) return (void *) body;
   if (strcmp(name,"quat") == 0) return (void *) quat;
+  if (strcmp(name,"temperature") == 0) return (void *) temperature;
+  if (strcmp(name,"heatflow") == 0) return (void *) heatflow;
 
   // PERI PACKAGE
 
@@ -3018,6 +3034,8 @@ int Atom::extract_datatype(const char *name)
   if (strcmp(name,"tri") == 0) return LAMMPS_INT;
   if (strcmp(name,"body") == 0) return LAMMPS_INT;
   if (strcmp(name,"quat") == 0) return LAMMPS_DOUBLE_2D;
+  if (strcmp(name,"temperature") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"heatflow") == 0) return LAMMPS_DOUBLE;
 
   if (strcmp(name,"vfrac") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"s0") == 0) return LAMMPS_DOUBLE;

src/atom.h

@@ -83,6 +83,7 @@ class Atom : protected Pointers {
   double **omega, **angmom, **torque;
   int *ellipsoid, *line, *tri, *body;
   double **quat;
+  double *temperature, *heatflow;
 
   // molecular systems
 
@@ -186,6 +187,7 @@ class Atom : protected Pointers {
   int molecule_flag, molindex_flag, molatom_flag;
   int q_flag, mu_flag;
   int rmass_flag, radius_flag, omega_flag, torque_flag, angmom_flag, quat_flag;
+  int temperature_flag, heatflow_flag;
   int vfrac_flag, spin_flag, eradius_flag, ervel_flag, erforce_flag;
   int cs_flag, csforce_flag, vforce_flag, ervelforce_flag, etag_flag;
   int rho_flag, esph_flag, cv_flag, vest_flag;

src/dump_custom.cpp

@@ -41,7 +41,7 @@ enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS,
      XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
      IX,IY,IZ,
      VX,VY,VZ,FX,FY,FZ,
-     Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
+     Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,HEATFLOW,TEMPERATURE,
      OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
      TQX,TQY,TQZ,
      COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY};
@@ -931,6 +931,18 @@ int DumpCustom::count()
         for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
         ptr = dchoose;
         nstride = 1;
+      } else if (thresh_array[ithresh] == HEATFLOW) {
+        if (!atom->heatflow_flag)
+          error->all(FLERR,
+                     "Threshold for an atom property that isn't allocated");
+        ptr = atom->heatflow;
+        nstride = 1;
+      } else if (thresh_array[ithresh] == TEMPERATURE) {
+        if (!atom->temperature_flag)
+          error->all(FLERR,
+                     "Threshold for an atom property that isn't allocated");
+        ptr = atom->temperature;
+        nstride = 1;
       } else if (thresh_array[ithresh] == OMEGAX) {
         if (!atom->omega_flag)
           error->all(FLERR,
@@ -1385,6 +1397,16 @@ int DumpCustom::parse_fields(int narg, char **arg)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
       pack_choice[iarg] = &DumpCustom::pack_diameter;
       vtype[iarg] = Dump::DOUBLE;
+    } else if (strcmp(arg[iarg],"heatflow") == 0) {
+      if (!atom->heatflow_flag)
+        error->all(FLERR,"Dumping an atom property that isn't allocated");
+      pack_choice[iarg] = &DumpCustom::pack_heatflow;
+      vtype[iarg] = Dump::DOUBLE;
+    } else if (strcmp(arg[iarg],"temperature") == 0) {
+      if (!atom->temperature_flag)
+        error->all(FLERR,"Dumping an atom property that isn't allocated");
+      pack_choice[iarg] = &DumpCustom::pack_temperature;
+      vtype[iarg] = Dump::DOUBLE;
     } else if (strcmp(arg[iarg],"omegax") == 0) {
       if (!atom->omega_flag)
         error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1850,6 +1872,8 @@ int DumpCustom::modify_param(int narg, char **arg)
 
     else if (strcmp(arg[1],"radius") == 0) thresh_array[nthresh] = RADIUS;
     else if (strcmp(arg[1],"diameter") == 0) thresh_array[nthresh] = DIAMETER;
+    else if (strcmp(arg[1],"heatflow") == 0) thresh_array[nthresh] = HEATFLOW;
+    else if (strcmp(arg[1],"temperature") == 0) thresh_array[nthresh] = TEMPERATURE;
     else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX;
     else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY;
     else if (strcmp(arg[1],"omegaz") == 0) thresh_array[nthresh] = OMEGAZ;
@@ -2764,6 +2788,30 @@ void DumpCustom::pack_diameter(int n)
 
 /* ---------------------------------------------------------------------- */
 
+void DumpCustom::pack_heatflow(int n)
+{
+  double *heatflow = atom->heatflow;
+
+  for (int i = 0; i < nchoose; i++) {
+    buf[n] = heatflow[clist[i]];
+    n += size_one;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpCustom::pack_temperature(int n)
+{
+  double *temperature = atom->temperature;
+
+  for (int i = 0; i < nchoose; i++) {
+    buf[n] = temperature[clist[i]];
+    n += size_one;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpCustom::pack_omegax(int n)
 {
   double **omega = atom->omega;

src/dump_custom.h

@@ -188,6 +188,8 @@ class DumpCustom : public Dump {
   void pack_mu(int);
   void pack_radius(int);
   void pack_diameter(int);
+  void pack_heatflow(int);
+  void pack_temperature(int);
 
   void pack_omegax(int);
   void pack_omegay(int);

src/fix_neigh_history.cpp

@@ -337,6 +337,7 @@ void FixNeighHistory::pre_exchange_newton()
   int *ilist,*jlist,*numneigh,**firstneigh;
   int *allflags;
   double *allvalues,*onevalues,*jvalues;
+  int *type = atom->type;
 
   // NOTE: all operations until very end are with
   //   nlocal_neigh  <= current nlocal and nall_neigh
@@ -351,7 +352,10 @@ void FixNeighHistory::pre_exchange_newton()
   // 1st loop over neighbor list
   // calculate npartner for owned+ghost atoms
 
-  for (i = 0; i < nall_neigh; i++) npartner[i] = 0;
+  // Ensure npartner is zeroed across all atoms, nall_neigh can be less than nall
+  // when writing restarts when comm calls are made but modify->post_neighbor() isn't
+  int nall = atom->nlocal + atom->nghost;
+  for (i = 0; i < MAX(nall_neigh, nall); i++) npartner[i] = 0;
 
   tagint *tag = atom->tag;
   NeighList *list = pair->list;
@@ -406,7 +410,7 @@ void FixNeighHistory::pre_exchange_newton()
   // store partner IDs and values for owned+ghost atoms
   // re-zero npartner to use as counter
 
-  for (i = 0; i < nall_neigh; i++) npartner[i] = 0;
+  for (i = 0; i < MAX(nall_neigh, nall); i++) npartner[i] = 0;
 
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
@@ -427,7 +431,7 @@ void FixNeighHistory::pre_exchange_newton()
         partner[j][m] = tag[i];
         jvalues = &valuepartner[j][dnum*m];
         if (pair->nondefault_history_transfer)
-          pair->transfer_history(onevalues,jvalues);
+          pair->transfer_history(onevalues,jvalues,type[i],type[j]);
         else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n];
       }
     }
@@ -466,6 +470,7 @@ void FixNeighHistory::pre_exchange_no_newton()
   int *ilist,*jlist,*numneigh,**firstneigh;
   int *allflags;
   double *allvalues,*onevalues,*jvalues;
+  int *type = atom->type;
 
   // NOTE: all operations until very end are with nlocal_neigh <= current nlocal
   // because previous neigh list was built with nlocal_neigh
@@ -541,7 +546,7 @@ void FixNeighHistory::pre_exchange_no_newton()
           partner[j][m] = tag[i];
           jvalues = &valuepartner[j][dnum*m];
           if (pair->nondefault_history_transfer)
-            pair->transfer_history(onevalues, jvalues);
+            pair->transfer_history(onevalues, jvalues,type[i],type[j]);
           else for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n];
         }
       }

src/fix_property_atom.cpp

@@ -25,7 +25,7 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
-enum { MOLECULE, CHARGE, RMASS, IVEC, DVEC, IARRAY, DARRAY };
+enum { MOLECULE, CHARGE, RMASS, TEMPERATURE, HEATFLOW, IVEC, DVEC, IARRAY, DARRAY };
 
 /* ---------------------------------------------------------------------- */
 
@@ -46,6 +46,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   molecule_flag = 0;
   q_flag = 0;
   rmass_flag = 0;
+  temperature_flag = 0;
+  heatflow_flag = 0;
 
   nvalue = 0;
   values_peratom = 0;
@@ -81,6 +83,26 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
       values_peratom++;
       nvalue++;
       iarg++;
+    } else if (strcmp(arg[iarg], "temperature") == 0) {
+      if (atom->temperature_flag)
+        error->all(FLERR, "Fix property/atom temperature when atom_style already has temperature attribute");
+      if (temperature_flag) error->all(FLERR, "Fix property/atom cannot specify temperature twice");
+      styles[nvalue] = TEMPERATURE;
+      cols[nvalue] = 0;
+      atom->temperature_flag = temperature_flag = 1;
+      values_peratom++;
+      nvalue++;
+      iarg++;
+    } else if (strcmp(arg[iarg], "heatflow") == 0) {
+      if (atom->heatflow_flag)
+        error->all(FLERR, "Fix property/atom heatflow when atom_style already has heatflow attribute");
+      if (heatflow_flag) error->all(FLERR, "Fix property/atom cannot specify heatflow twice");
+      styles[nvalue] = HEATFLOW;
+      cols[nvalue] = 0;
+      atom->heatflow_flag = heatflow_flag = 1;
+      values_peratom++;
+      nvalue++;
+      iarg++;
 
       // custom atom vector
 
@@ -163,14 +185,15 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
 
   if (border) comm_border = values_peratom;
 
-  // warn if mol or charge keyword used without ghost yes
+  // warn if mol, charge, rmass, temperature, or heatflow keyword used without ghost yes
 
   if (border == 0) {
     int flag = 0;
     for (int i = 0; i < nvalue; i++)
-      if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS) flag = 1;
+      if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS ||
+      styles[i] == TEMPERATURE || styles[i] == HEATFLOW) flag = 1;
     if (flag && comm->me == 0)
-      error->warning(FLERR, "Fix property/atom mol or charge or rmass w/out ghost communication");
+      error->warning(FLERR, "Fix property/atom mol, charge, rmass, temperature, or heatflow w/out ghost communication");
   }
 
   // store current atom style
@@ -213,6 +236,14 @@ FixPropertyAtom::~FixPropertyAtom()
       atom->rmass_flag = 0;
       memory->destroy(atom->rmass);
       atom->rmass = nullptr;
+    } else if (styles[nv] == TEMPERATURE) {
+      atom->temperature_flag = 0;
+      memory->destroy(atom->temperature);
+      atom->temperature = nullptr;
+    } else if (styles[nv] == HEATFLOW) {
+      atom->heatflow_flag = 0;
+      memory->destroy(atom->heatflow);
+      atom->heatflow = nullptr;
     } else if (styles[nv] == IVEC) {
       atom->remove_custom(index[nv], 0, cols[nv]);
     } else if (styles[nv] == DVEC) {
@@ -298,6 +329,10 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
             atom->q[m] = values.next_double();
           } else if (styles[j] == RMASS) {
             atom->rmass[m] = values.next_double();
+          } else if (styles[j] == TEMPERATURE) {
+            atom->temperature[m] = values.next_double();
+          } else if (styles[j] == HEATFLOW) {
+            atom->heatflow[m] = values.next_double();
           } else if (styles[j] == IVEC) {
             atom->ivector[index[j]][m] = values.next_int();
           } else if (styles[j] == DVEC) {
@@ -377,6 +412,14 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
       double *rmass = atom->rmass;
       for (i = 0; i < nlocal; i++) buf[i][icol] = rmass[i];
       icol++;
+    } else if (styles[nv] == TEMPERATURE) {
+      double *temperature = atom->temperature;
+      for (i = 0; i < nlocal; i++) buf[i][icol] = temperature[i];
+      icol++;
+    } else if (styles[nv] == HEATFLOW) {
+      double *heatflow = atom->heatflow;
+      for (i = 0; i < nlocal; i++) buf[i][icol] = heatflow[i];
+      icol++;
     } else if (styles[nv] == IVEC) {
       int *ivec = atom->ivector[index[nv]];
       for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(ivec[i]).d;
@@ -424,6 +467,10 @@ void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
         fputs(" q", fp);
       else if (styles[i] == RMASS)
         fputs(" rmass", fp);
+      else if (styles[i] == TEMPERATURE)
+        fputs(" temperature", fp);
+      else if (styles[i] == HEATFLOW)
+        fputs(" heatflow", fp);
       else if (styles[i] == IVEC)
         fprintf(fp, " i_%s", atom->ivname[index[i]]);
       else if (styles[i] == DVEC)
@@ -459,6 +506,10 @@ void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp, int n, double **
         line += fmt::format(" {}", buf[i][icol++]);
       else if (styles[nv] == RMASS)
         line += fmt::format(" {}", buf[i][icol++]);
+      else if (styles[nv] == TEMPERATURE)
+        line += fmt::format(" {}", buf[i][icol++]);
+      else if (styles[nv] == HEATFLOW)
+        line += fmt::format(" {}", buf[i][icol++]);
       else if (styles[nv] == IVEC)
         line += fmt::format(" {}", (int) ubuf(buf[i][icol++]).i);
       else if (styles[nv] == DVEC)
@@ -491,6 +542,10 @@ double FixPropertyAtom::memory_usage()
       bytes = atom->nmax * sizeof(double);
     else if (styles[m] == RMASS)
       bytes = atom->nmax * sizeof(double);
+    else if (styles[m] == TEMPERATURE)
+      bytes = atom->nmax * sizeof(double);
+    else if (styles[m] == HEATFLOW)
+      bytes = atom->nmax * sizeof(double);
     else if (styles[m] == IVEC)
       bytes = atom->nmax * sizeof(int);
     else if (styles[m] == DVEC)
@@ -525,6 +580,14 @@ void FixPropertyAtom::grow_arrays(int nmax)
       memory->grow(atom->rmass, nmax, "atom:rmass");
       size_t nbytes = (nmax - nmax_old) * sizeof(double);
       memset(&atom->rmass[nmax_old], 0, nbytes);
+    } else if (styles[nv] == TEMPERATURE) {
+      memory->grow(atom->temperature, nmax, "atom:temperature");
+      size_t nbytes = (nmax - nmax_old) * sizeof(double);
+      memset(&atom->temperature[nmax_old], 0, nbytes);
+    } else if (styles[nv] == HEATFLOW) {
+      memory->grow(atom->heatflow, nmax, "atom:heatflow");
+      size_t nbytes = (nmax - nmax_old) * sizeof(double);
+      memset(&atom->heatflow[nmax_old], 0, nbytes);
     } else if (styles[nv] == IVEC) {
       memory->grow(atom->ivector[index[nv]], nmax, "atom:ivector");
       size_t nbytes = (nmax - nmax_old) * sizeof(int);
@@ -562,6 +625,10 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
       atom->q[j] = atom->q[i];
     else if (styles[nv] == RMASS)
       atom->rmass[j] = atom->rmass[i];
+    else if (styles[nv] == TEMPERATURE)
+      atom->temperature[j] = atom->temperature[i];
+    else if (styles[nv] == HEATFLOW)
+      atom->heatflow[j] = atom->heatflow[i];
     else if (styles[nv] == IVEC)
       atom->ivector[index[nv]][j] = atom->ivector[index[nv]][i];
     else if (styles[nv] == DVEC)
@@ -604,6 +671,18 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
         j = list[i];
         buf[m++] = rmass[j];
       }
+    } else if (styles[nv] == TEMPERATURE) {
+      double *temperature = atom->temperature;
+      for (i = 0; i < n; i++) {
+        j = list[i];
+        buf[m++] = temperature[j];
+      }
+    } else if (styles[nv] == HEATFLOW) {
+      double *heatflow = atom->heatflow;
+      for (i = 0; i < n; i++) {
+        j = list[i];
+        buf[m++] = heatflow[j];
+      }
     } else if (styles[nv] == IVEC) {
       int *ivector = atom->ivector[index[nv]];
       for (i = 0; i < n; i++) {
@@ -658,6 +737,14 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
       double *rmass = atom->rmass;
       last = first + n;
       for (i = first; i < last; i++) rmass[i] = buf[m++];
+    } else if (styles[nv] == TEMPERATURE) {
+      double *temperature = atom->temperature;
+      last = first + n;
+      for (i = first; i < last; i++) temperature[i] = buf[m++];
+    } else if (styles[nv] == HEATFLOW) {
+      double *heatflow = atom->heatflow;
+      last = first + n;
+      for (i = first; i < last; i++) heatflow[i] = buf[m++];
     } else if (styles[nv] == IVEC) {
       int *ivector = atom->ivector[index[nv]];
       last = first + n;
@@ -700,6 +787,10 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
       buf[m++] = atom->q[i];
     else if (styles[nv] == RMASS)
       buf[m++] = atom->rmass[i];
+    else if (styles[nv] == TEMPERATURE)
+      buf[m++] = atom->temperature[i];
+    else if (styles[nv] == HEATFLOW)
+      buf[m++] = atom->heatflow[i];
     else if (styles[nv] == IVEC)
       buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
     else if (styles[nv] == DVEC)
@@ -732,6 +823,10 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
       atom->q[nlocal] = buf[m++];
     else if (styles[nv] == RMASS)
       atom->rmass[nlocal] = buf[m++];
+    else if (styles[nv] == TEMPERATURE)
+      atom->temperature[nlocal] = buf[m++];
+    else if (styles[nv] == HEATFLOW)
+      atom->heatflow[nlocal] = buf[m++];
     else if (styles[nv] == IVEC)
       atom->ivector[index[nv]][nlocal] = (int) ubuf(buf[m++]).i;
     else if (styles[nv] == DVEC)
@@ -768,6 +863,10 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
       buf[m++] = atom->q[i];
     else if (styles[nv] == RMASS)
       buf[m++] = atom->rmass[i];
+    else if (styles[nv] == TEMPERATURE)
+      buf[m++] = atom->temperature[i];
+    else if (styles[nv] == HEATFLOW)
+      buf[m++] = atom->heatflow[i];
     else if (styles[nv] == IVEC)
       buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
     else if (styles[nv] == DVEC)
@@ -807,6 +906,10 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
       atom->q[nlocal] = extra[nlocal][m++];
     else if (styles[nv] == RMASS)
       atom->rmass[nlocal] = extra[nlocal][m++];
+    else if (styles[nv] == TEMPERATURE)
+      atom->temperature[nlocal] = extra[nlocal][m++];
+    else if (styles[nv] == HEATFLOW)
+      atom->heatflow[nlocal] = extra[nlocal][m++];
     else if (styles[nv] == IVEC)
       atom->ivector[index[nv]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
     else if (styles[nv] == DVEC)

src/fix_property_atom.h

@@ -54,6 +54,7 @@ class FixPropertyAtom : public Fix {
  protected:
   int nvalue, border;
   int molecule_flag, q_flag, rmass_flag;    // flags for specific fields
+  int temperature_flag, heatflow_flag;
   int *styles;                              // style of each value, see enum
   int *index;                               // indices into atom custom data structs
   int *cols;                                // columns per value, for arrays

src/pair.h

@@ -223,7 +223,7 @@ class Pair : protected Pointers {
   virtual void min_xf_pointers(int, double **, double **) {}
   virtual void min_xf_get(int) {}
   virtual void min_x_set(int) {}
-  virtual void transfer_history(double *, double *) {}
+  virtual void transfer_history(double *, double *, int, int) {}
   virtual double atom2cut(int) { return 0.0; }
   virtual double radii2cut(double, double) { return 0.0; }
 

src/set.cpp

@@ -47,7 +47,7 @@ enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
 enum{TYPE,TYPE_FRACTION,TYPE_RATIO,TYPE_SUBSET,
      MOLECULE,X,Y,Z,VX,VY,VZ,CHARGE,MASS,SHAPE,LENGTH,TRI,
      DIPOLE,DIPOLE_RANDOM,SPIN_ATOM,SPIN_RANDOM,SPIN_ELECTRON,RADIUS_ELECTRON,
-     QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,
+     QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,TEMPERATURE,
      DIAMETER,RADIUS_ATOM,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
      SPH_E,SPH_CV,SPH_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY,
      SMD_CONTACT_RADIUS,DPDTHETA,EPSILON,IVEC,DVEC,IARRAY,DARRAY};
@@ -426,6 +426,15 @@ void Set::command(int narg, char **arg)
       set(DENSITY);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"temperature") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+      if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
+      else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
+      if (!atom->temperature_flag)
+        error->all(FLERR,"Cannot set this attribute for this atom style");
+      set(TEMPERATURE);
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"volume") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set volume", error);
       if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
@@ -806,6 +815,7 @@ void Set::set(int keyword)
   case SHAPE:
   case DIAMETER:
   case DENSITY:
+  case TEMPERATURE:
   case QUAT:
   case IMAGE:
     if (modify->check_rigid_list_overlap(select))
@@ -1068,6 +1078,13 @@ void Set::set(int keyword)
       atom->omega[i][2] = zvalue;
     }
 
+    // set temperature of particle
+
+    else if (keyword == ANGMOM) {
+      if (dvalue < 0.0) error->one(FLERR,"Invalid temperature in set command");
+      atom->temperature[i] = dvalue;
+    }
+
     // reset any or all of 3 image flags
 
     else if (keyword == IMAGE) {