Compilation errors

doc/src/Commands_fix.rst

@@ -234,6 +234,8 @@ OPT.
    * :doc:`srd <fix_srd>`
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
+   * :doc:`surface/global <fix_surface_global>`
+   * :doc:`surface/local <fix_surface_local>`
    * :doc:`tdpd/source <fix_dpd_source>`
    * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`

doc/src/Howto.rst

@@ -23,7 +23,6 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
-   Howto_broken_bonds
 
 Settings howto
 ==============
@@ -49,6 +48,7 @@ Analysis howto
    :maxdepth: 1
 
    Howto_output
+   Howto_structured_data
    Howto_chunk
    Howto_grid
    Howto_temperature
@@ -56,7 +56,6 @@ Analysis howto
    Howto_kappa
    Howto_viscosity
    Howto_diffusion
-   Howto_structured_data
 
 Force fields howto
 ==================
@@ -65,6 +64,7 @@ Force fields howto
    :name: force_howto
    :maxdepth: 1
 
+   Howto_broken_bonds
    Howto_bioFF
    Howto_amoeba
    Howto_tip3p
@@ -81,6 +81,7 @@ Packages howto
 
    Howto_spherical
    Howto_granular
+   Howto_granular_surfaces
    Howto_body
    Howto_bpm
    Howto_polarizable

doc/src/Howto_granular.rst

@@ -1,10 +1,28 @@
 Granular models
 ===============
 
-Granular system are composed of spherical particles with a diameter,
+Granular systems are composed of spherical particles with a diameter,
 as opposed to point particles.  This means they have an angular
 velocity and torque can be imparted to them to cause them to rotate.
 
+The various atom, pair, fix, and compute styles listed below are
+useful for creaeting granular models.
+
+You can also define granular surfaces which are a collection of line
+segments (2d systems) or triangles (3d systems), which act as
+boundaries interacting with the particles.  Particle/surface
+interactions can be specified with similar options as the pair styles
+listed below.
+
+This Howto doc page and two fixes explain how to define and use
+granular surfaces:
+
+* :doc:`Howto granular surfaces <Howto_granular_surfaces>`
+* :doc:`fix surface/global <fix_surface_global>`
+* :doc:`fix surface/local <fix_surface_local>`
+
+----------
+
 To run a simulation of a granular model, you will want to use
 the following commands:
 
@@ -16,12 +34,15 @@ This compute
 
 * :doc:`compute erotate/sphere <compute_erotate_sphere>`
 
-calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
-The compute
+calculates rotational kinetic energy which can be :doc:`output with
+thermodynamic info <Howto_output>`.
+
+This compute
 
 * :doc:`compute fabric <compute_fabric>`
 
-calculates various versions of the fabric tensor for granular and non-granular pair styles.
+calculates various versions of the fabric tensor for granular and
+non-granular pair styles.
 
 Use one of these 4 pair potentials, which compute forces and torques
 between interacting pairs of particles:
@@ -31,8 +52,13 @@ between interacting pairs of particles:
 * :doc:`pair_style gran/hertzian <pair_gran>`
 * :doc:`pair_style granular <pair_granular>`
 
+To add your own custom granular contact model to the :doc:`pair_style
+granular <pair_granular>` command, see the :doc:`Modifying granular
+sub-models <Modify_gran_sub_mod>` doc page.
+
 These commands implement fix options specific to granular systems:
 
+* :doc:`fix freeze <fix_freeze>`
 * :doc:`fix freeze <fix_freeze>`
 * :doc:`fix pour <fix_pour>`
 * :doc:`fix viscous <fix_viscous>`
@@ -69,6 +95,3 @@ 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/Howto_granular_surfaces.rst

@@ -0,0 +1,289 @@
+Granular surfaces
+=================
+
+As explained on the :doc:`Howto granular <Howto_granular>` doc page,
+granular systems are composed of spherical particles with a diameter,
+as opposed to point particles.  This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+
+The :doc:`Howto granular <Howto_granular>` doc page lists various
+atom, pair, fix, and compute styles useful for creaeting granular
+models.
+
+This page explains how you can also define granular surfaces which are
+a collection of triangles (3d systems) or line segments (2d systems),
+which act as boundaries interacting with the particles.  Different
+kinds of particle/surface interactions can be specified with similar
+options as the pair styles listed on the :doc:`Howto granular
+<Howto_granular>` doc page.
+
+----------
+
+Global versus local surfaces
+""""""""""""""""""""""""""""
+A key point to understand is that LAMMPS supports two forms of
+granular surfaces.  You cannot use both in the same simulation.
+
+The first is *global* which means that each processor stores a copy of
+all the triangles/lines.  This is suitable when a modest number of
+triangles/lines is needed.  They can be large triangles/lines, any of
+which span a significant fraction of the simulation box size in one or
+more dimensions.
+
+The second is *local* which means that the collection of
+triangles/lines is distributed across processers in the same manner
+that particles are distributed.  Each processor is assigned to
+sub-domain of the simulation box and owns whichever triangles/lines
+have their center point in the processor's sub-domain.  Similar to
+particles, each processor may also own ghost copies of triangles/lines
+whose finite size overlaps with the processor's sub-domain.  The
+number of triangles/lines can now be very large.  For effective
+distribution and minimal communication all the triangles/lines should
+be small, no more than a few particle diameters in size.  If even one
+larger triangle or line is defined then the neighbor list cutoff and
+communication cutoff will be set correspondingly larger, which can
+slow down the simulation.
+
+One of these two commands must be specified to use *global* or *local*
+surfaces in your granular simulation:
+
+* :doc:`fix surface/global <fix_surface_global>`
+* :doc:`fix surface/local <fix_surface_local>`
+
+The :doc:`fix surface/global <fix_surface_global>` command reads in
+the global surfaces in one of two ways.  The first option is from a
+molecule file(s) previously defined by the :doc:`molecule <molecule>`
+command.  The file should define triangles or lines with header
+keywords and a Triangles or Lines section.  The second option is from
+a text or binary STL (strereolithogray) file which defines a set of
+triangles.  It can only be used with 3d simulations.
+
+The :doc:`fix surface/local <fix_surface_local>` command defines local
+surface in one of three ways.  The first two options are the same
+molecule and STL files explained in the previous paragraph.  In this
+case, the list of triangles/lines is distributed across processors
+based on the center point of each triangle/line.  The third option is
+to include them in a LAMMPS data file which has been previously read
+in via the :doc:`read_data <read_data>` command.  If the file has a
+Triangles or Lines section, then triangles/lines will be read in and
+distributed along with any particles the data file includes.
+
+----------
+
+Surface attributes
+""""""""""""""""""
+
+For both global and local surfaces, each triangle/line is assigned a
+*type* and a *molecule ID*.  This is done when surfaces are read-in
+from a molecule, STL, or data file.  Since STL files do not define
+types or molecule IDs, the :doc:`fix surface/global
+<fix_surface_global>` and :doc:`fix surface/local <fix_surface_local>`
+commands specify the type that will be assigned to the read-in
+triangles.  The molecule ID for each triangle is set to 1.  The
+:doc:`fix surface/global <fix_surface_global>` command also allows use
+of the :doc:`fix_modify type/region <fix_modify>` command to assign
+types based on a geometric region.  Since local surfaces are
+effectively particles, the :doc:`set <set>` command can be used to
+alter the *type* or *molecule ID* of any triangle or line.
+
+For both global and local surfaces, types are used to define the style
+of granular interactions for individual triangles/lines.  Different
+styles can be used within a single object consisting of connected
+triangles/lines.  See the Surface Connectivity section below.
+
+Molecule IDs are not currently used by granular surface interactions,
+though they may be in the future.  They are intended to be assigned
+uniquely to each inter-connected set of triangles/lines, as if each
+object were a "molecule".  However, this is not required, and LAMMPS
+does not check that this is the case.  LAMMPS will issue a warning if
+a set of inter-connected triangles/lines do not all have the same
+molecule ID, in case this was not intentional.
+
+For local surfaces, the molecule ID can be used to define groups and
+thus assign different motions to different surface objects.  See the
+Surface Motion section below.  Various other LAMMPS commands operate
+on groups or molecules and can thus be used to gather statistics about
+or output information about individual surface objects.
+
+----------
+
+Atom styles for granular surfaces
+"""""""""""""""""""""""""""""""""
+
+For all three ways of defining *local* surfaces, the triangles/lines
+are stored internally in LAMMPS as triangle-style or line-style
+particles.  This means you must use a hybrid atom style which includes
+one of these two sub-styles (for 3d or 2d):
+
+* :doc:`atom_style tri <atom_style>` for 3d simulations
+* :doc:`atom_style line <atom_style>` for 2d simulations
+
+Typically, the atom_style hybrid command will also define a
+:doc:`atom_style sphere <atom_style>` sub-style for the granular
+particles which interact with the surfaces.
+
+Note that for molecule or STL file input, the :doc:`fix surface/local
+<fix_surface_local>` command reads the file(s) and uses the values for
+each surface to creat a single new triangle or line particle.  For
+data file input, the triangle/line particles are created when the data
+file is read.
+
+For granular simluations with *global* surfaces, a hybrid atom style
+which defines triangle-style or line-style particles should NOT be
+used.  The triangles/lines are stored by the :doc:`fix surface/global
+<fix_surface_global>` command and not as triangle-style or line-style
+particles.
+
+----------
+
+Rules for surface topology
+""""""""""""""""""""""""""
+
+For both *global* and *local* surfaces, granular particles interact
+with both sides of each triangle or line segment.
+
+No check is made to see if two triangles or line segments intersect
+each other; this is allowed if it makes sense for the geometry of the
+collection of surfaces.
+
+As an example, consider a 2d simulation which mixes a container of
+granular particles.  *Global* line segments are used to define both
+the box-shaped container and the mixer in the center.  The 4 mixer
+blades are in the shape of a large X and are made to rotate using the
+:doc:`fix_modify <fix_modify>` command (see below).
+
+The 2 blades could be defined by 2 line segments which cross each
+other at their centers.  Or the 2 blades could be defined by 4 line
+segments, all of which have a common endpoint at the center of the
+mixer.  Or the 2 blades could be defined by 4 non-touching line
+segments, all of which have a distinct endpoint near the center of the
+mixer, but displaced from it by a distance less than the radius of a
+granular particle.  In any of these cases, when a particle gets very
+close to the center of the mixer it will interact with both nearby
+line segments as expected.
+
+See the next section on connectivity for how two triangles or line
+segemnts are treated if they share a common edge (triangle) or point
+(triange or line).
+
+----------
+
+Surface connectivity
+""""""""""""""""""""
+
+If multiple triangles/lines are used to define a contiguous surface
+which is flat or gently curved or has sharp edges or corners, LAMMPS
+will detect when two or more line segments (2d) share the same
+endpoint.  Or when two or more triangles (3d) share the same edge or
+same corner point.
+
+This connectivity is stored internally and is used when appropriate to
+calculate accurate forces on particles which simultaneously overlap
+with 2 or more connected triangles or line segments.
+
+Consider the simulation model of the previous section for a 2d mixer
+now defined by *local* line segments.  The flat surface of each mixer
+blade (and container box faces) is defined by multiple small line
+segments.  It is imporant that these line segments be "connected" so
+that when a particle contacts two adjacent line segments at the same
+time, the resulting force on the particle is the same as it would be
+if it were contacting the middle of a single long line segment.
+
+Here is how to ensure that LAMMPS detects the appropriate connections.
+
+For either *global* or *local* surfaces, if the triangles/lines are
+defined in a molecule or STL file, then 3 corner points (triangle) or
+2 end points (line) will be listed for each triangle/line in the file.
+LAMMPS will only make a connection between 2 triangles or lines if a
+shared point is EXACTLY the same in both.  This is a single point in
+both for a corner point or end point connection.  It is two points in
+both triangles for an edge connection.
+
+For *local* surfaces, if the triangles/lines are defined in a data
+file, then 3 corner points (triangle) or 2 end points (line) will be
+listed for each triangle/line in the file.  However in this case,
+LAMMPS will allow for an INEXACT match of a shared point to make a
+connection between 2 triangles or lines.  Again, this is a single
+point in both for a corner point or end point connection.  It is two
+points in both triangles for an edge connection.
+
+An INEXACT match means that the two points can be EPSILON apart.
+EPSILON is defined as a tiny fraction (1.0e-4) of the size of
+the smallest triangle or line in the system.
+
+The reason INEXACT matches are allowed is that data files can be
+created in a variety of manners, including by LAMMPS itself as a
+simulation runs via the :doc:`write_data <write_data>` command.
+Interally, triangle-style and line-style particles do not store their
+corner points directly.  Instead, the center point of the
+triangle/line is stored, along with an orientation of the
+triangle/line and a displacement vector from the center point for each
+corner point.  This means that when new corner points values are
+written to a data file for two different triangles/line, they may
+differ by epsilon due to round-offs in finite-precision arithmetic.
+
+Note that due to how connectivity is defined, two triangles/lines will
+not be connected if their corner points are separted by even small
+distances (greater than EPSILON).  Likewise they will not be connected
+if the corner point of one triangle/line is very close to (or even on)
+the surface of another triangle or middle of another line segment.  In
+general these kinds of granular surfaces could be problematic and
+should be avoided, but LAMMPS does not check for these conditions.
+
+NOTE: maybe add a picture of T-shaped surf with 2 line segments (not
+3).  Explain why it could be bad?
+
+Note that if a triangle or line segment has a free edge or free
+corner/end point (not connected to any other triangle/line), granular
+particles will still interact with the triangle/line if the nearest
+contact point to the spherical particle center is on the free edge or
+is the free corner/end point.
+
+----------
+
+Surface motion
+""""""""""""""
+
+By default, surface triangles/lines are motionless during a
+simulation, whether they are *global* or *local*.  Triangles/lines
+impart forces and torques to granular particles, but the inverse
+forces/torques on the triangles/lines do not cause them to move.
+
+However, triangles/lines can be made to move in a prescribed manner.
+E.g. the rotation of 2d mixer blades in the example described above.
+These two commands can be used for that purpose:
+
+* :doc:`fix_modify move <fix_modify>` for *global* surfaces
+* :doc:`fix move <fix_move>` for *local* surfaces
+
+For *global* surfaces, the :doc:`fix_modify move <fix_modify>` command
+can move a specified subest of the triangles/lines in various ways
+(translation, rotation, etc).  Which triangles move is specified based
+on the *type* of each triangle.  Types are specified when surfaces are
+defined by the :doc:`fix surface/global <fix_surface_global>` command.
+They can also be defined by the :doc:`fix_modify typre/region
+<fix_modify>` command.
+
+For *local* surfaces, the :doc:`fix move <fix_move>` command can move
+a specified subset of the triangles/lines in various ways
+(translation, rotation, etc).  Which triangles move is specified based
+on the group-ID argument to the :doc:`fix move <fix_move>` command.
+Groups can be defined by the :doc:`group <group>` command.
+
+Note that for an object defined by two or more connected
+triangles/lines, it is an error to assign a motion and not include all
+the connected triangles/lines, since this would break the connections.
+LAMMPS does NOT check that this requirement is met.
+
+----------
+
+Example scripts
+"""""""""""""""
+
+The examples/gransurf directory has example input scripts which use
+both *global* and *local* surfaces.  Both 2d and 3d models are included.
+
+Each script produces a series of snapshot images using the :doc:`dump
+image <dump_image>` command.  The snapshots visualize both the
+particles and granular surfaces.  The snaphost can be animated to view
+a movie of the simulation.

doc/src/Packages_details.rst

@@ -61,6 +61,7 @@ gives those details.
    * :ref:`FEP <PKG-FEP>`
    * :ref:`GPU <PKG-GPU>`
    * :ref:`GRANULAR <PKG-GRANULAR>`
+   * :ref:`GRANSURF <PKG-GRANSURF>`
    * :ref:`H5MD <PKG-H5MD>`
    * :ref:`INTEL <PKG-INTEL>`
    * :ref:`INTERLAYER <PKG-INTERLAYER>`
@@ -1099,6 +1100,31 @@ potentials.
 
 ----------
 
+.. _PKG-GRANSURF:
+
+GRANSURF package
+----------------
+
+**Contents:**
+
+Granular surfaces consisting of triangles (3d) or line segments (2d).
+These interact with finite-size granular particles as static or moving
+boundary conditions and support the same kind of interaction models as
+granular pair styles do for particle/particle interactions.  The
+collection of triangles or lines can be "global" with each processor
+storing all of them.  Or it can be "local" where the triangles/lines
+are distributed across processors.
+
+**Supporting info:**
+
+* src/GRANSURF: filenames -> commands
+* :doc:`Howto granular surfaces <Howto_granular_surfaces>`
+* :doc:`fix surface/global <fix_surface_global>`
+* :doc:`fix surface_local <fix_surface_local>`
+* examples/gransurf
+
+----------
+
 .. _PKG-H5MD:
 
 H5MD package

doc/src/Packages_list.rst

@@ -203,6 +203,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`Howto granular <Howto_granular>`
      - pour
      - no
+   * - :ref:`GRANSURF <PKG-GRANSURF>`
+     - granular surfaces
+     - :doc:`Howto granular surfaces <Howto_granular_surfaces>`
+     - pour
+     - no
    * - :ref:`H5MD <PKG-H5MD>`
      - dump output via HDF5
      - :doc:`dump h5md <dump_h5md>`

doc/src/fix.rst

@@ -413,6 +413,8 @@ accelerated styles exist.
 * :doc:`srd <fix_srd>` - stochastic rotation dynamics (SRD)
 * :doc:`store/force <fix_store_force>` - store force on each atom
 * :doc:`store/state <fix_store_state>` - store attributes for each atom
+* :doc:`surface/global <fix_surface_global>` - global granular surface model, each proc has copy
+* :doc:`surface/local <fix_surface_local>` - local granular surface model, distributed across procs
 * :doc:`tdpd/source <fix_dpd_source>` - add external concentration source
 * :doc:`temp/berendsen <fix_temp_berendsen>` - temperature control by Berendsen thermostat
 * :doc:`temp/csld <fix_temp_csvr>` - canonical sampling thermostat with Langevin dynamics

doc/src/fix_modify.rst

@@ -43,10 +43,12 @@ Examples
 Description
 """""""""""
 
-Modify one or more parameters of a previously defined fix.  Only
-specific fix styles support specific parameters.  See the doc pages
-for individual fix commands for info on which ones support which
-fix_modify parameters.
+Modify one or more parameters of a previously defined fix.  Specific
+fix styles support specific parameters.  See the doc pages of an
+individual fix command for info on which fix_modify keywords it
+supports.  This doc page only describes fix_modify keywords which are
+supported by multiple fixes.  Additional keywords, specific to a
+single fix, are only described on that fix's doc page.
 
 The *temp* keyword is used to determine how a fix computes
 temperature.  The specified compute ID must have been previously
@@ -171,7 +173,6 @@ will have no effect on the motion of the rigid bodies if they are
 specified in the input script after the fix rigid command.  LAMMPS
 will give a warning if that is the case.
 
-
 The *colname* keyword can be used to change the default header keywords
 in output files of fix styles that support it: currently only :doc:`fix
 ave/time <fix_ave_time>` is supported.  The setting for *ID string*
@@ -184,7 +185,6 @@ replaces the string for that specific keyword. The *colname* keyword can
 be used multiple times. If multiple *colname* settings refer to the same
 keyword, the last setting has precedence.
 
-
 Restrictions
 """"""""""""
 none

doc/src/fix_nve.rst

@@ -31,13 +31,13 @@ Description
 
 Perform plain time integration to update position and velocity for
 atoms in the group each timestep.  This creates a system trajectory
-consistent with the microcanonical ensemble (NVE) provided there
-are (full) periodic boundary conditions and no other "manipulations"
-of the system (e.g. fixes that modify forces or velocities).
+consistent with the microcanonical ensemble (NVE) provided there are
+(full) periodic boundary conditions and no other "manipulations" of
+the system (e.g. fixes that modify forces or velocities).
 
-This fix invokes the velocity form of the
-Stoermer-Verlet time integration algorithm (velocity-Verlet). Other
-time integration options can be invoked using the :doc:`run_style <run_style>` command.
+This fix invokes the velocity form of the Stoermer-Verlet time
+integration algorithm (velocity-Verlet). Other time integration
+options can be invoked using the :doc:`run_style <run_style>` command.
 
 ----------
 
@@ -48,15 +48,18 @@ time integration options can be invoked using the :doc:`run_style <run_style>` c
 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 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
- none
+
+none
 
 Related commands
 """"""""""""""""

doc/src/fix_surface_global.rst

@@ -0,0 +1,372 @@
+.. index:: fix surface/global
+
+fix surface/global command
+===============
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID surface/global input args input args ... model args model args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* surface/global = style name of this fix command
+* input = one or more input keywords can be specified
+
+  .. parsed-literal::
+
+       *input* args = source source-args
+         *source* = *mol* or *stl*
+            *mol* arg = template-ID
+               template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command, which defines a set of triangles or lines
+            *stl* args = stype stlfile
+               stype = numeric type assigned to all triangles in STL file
+               stlfile = STL filename which defines a set of triangles
+
+* model = one or more model keywords can be specified
+
+  .. parsed-literal::
+
+        *model* args = ptype stype fstyle fstyle-args
+           ptype = numeric particle type (see asterisk form below)
+           stype = numeric surface type (see asterisk form below)
+           *fstyle* =  *hooke* or *hooke/history* or *hertz/history* or *granular*
+             *hooke* or *hooke/history* or *hertz/history* args = Kn Kt gamma_n gamma_t xmu dampflag (limit_damping)
+                Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+                Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+                gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+                gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+                xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+                dampflag = 0 or 1 if tangential damping force is excluded or included
+                limit_damping = optional argument to prevent attractive interactions
+             *granular* args = same syntax for args as *pair_coeff* command of :doc:`pair_style granular <pair_granular>`
+
+* zero or more keyword/value pairs may be appended
+* keyword = *smax* or *flat* or *temperature*
+
+  .. parsed-literal::
+
+       *smax* value = smaxtype
+         smaxtype = maximum surface type allowed
+       *flat* value = maxangle
+         maxangle = maximum angle (degrees) between a pair of connected triangles/lines for a flat connection
+       *temperature* value = Tsurf
+         Tsurf = surface temperature (degrees Kelvin), required if model with heat is used
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   molecule lines surf.line
+   fix 1 all surface/global input mol linesurf model 1 1 hooke 4000.0 NULL 100.0 NULL 0.5 1
+
+   fix 1 all surface/global input stl 1 object.stl model * 1 hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+
+Description
+"""""""""""
+
+Enable granular surfaces to be used as boundary conditions on
+particles in a granular simulation.  Granular surfaces are defined as
+a set of triangles (3d) or a set of line segments (2d).
+
+The :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page
+gives an overview of granular surfaces of two types, *global* and
+*local*, with guidelines for how to use them.
+
+This command is used for models with *global* surfaces.  The :doc:`fix
+surface/local <fix_surface_local>` command is used for models with
+*local* surfaces.  As explained on the :doc:`Howto granular surfaces
+<Howto_granular_surfaces>` doc page, *global* surfaces are most
+appropriate when there is a modest number of them.  Each surface
+(triangle/line) can be of any size, even as large as a dimension of
+the simulation box.  A copy of the list of *global* surfaces is stored
+by each processor.
+
+*Global* triangles or line segments are not stored as particles and
+distributed across processors.  Rather, they are stored by this fix
+and each processor stores a copy of all of them.  This fix also
+computes forces between the global surfaces and all the particles.
+
+*Global* surfaces can be defined in 2 ways, which correspond to the 2
+options listed above for the *source* argument of the *input* keyword:
+
+* via a molecule file(s), read by the :doc:`molecule <molecule>` command
+* via an STL file(s), read by this command
+
+If triangles or lines were previously read in by the :doc:`molecule
+<molecule>` command, the *source* argument of the *input* keyword is
+*mol* and its *template-ID* argument is the molecule template ID used
+with the :doc:`molecule <molecule>` command.  Note that a
+doc:`molecule <molecule>` command can read and assign serveral
+molecule files to the same template-ID.  Each molecule file must
+define triangles or lines, not atoms.  For multiple molecule files,
+the set of triangles or lines defined used by this input option will
+be the union of the triangles and lines from all the molecule files.
+Note that each line/triangle in a molecule file is assigned a type and
+molecule ID.
+
+An STL (stereolithography) file defines a set of triangles.  For use
+with this command, the *source* argument of the *input* keyword is
+*stl*.  The *stype* argument is the numeric type assigned to all the
+triangles from the file.  Note that STL files do not contain types or
+other flags for each triangle.  The *stlfile* argument is the name of
+the STL file.  It can be in text or binary format; this command
+auto-detects the format.  Note that STL files cannot be used for 2d
+simulations since they only define triangles.  Each triangle from an
+STL file is assigned a molecule ID = 1.
+
+This `Wikepedia page
+<https://en.wikipedia.org/wiki/STL_(file_format)>`_ describes the
+format of both text and binary STL files.  Binary STL files can be
+converted to ASCII for editing with the stl_bin2txt tool in the
+lammps/tools directory.  Examples of text-based STL files are included
+in the examples/gransurf directory.
+
+Note that this command allows for multiple uses of the *input*
+keyword, each with a *source* argument as either *mol* or *stl*.  The
+surfaces used by this command are the union of the triangles and lines
+from all the input keywords.
+
+Once surfaces are defined, this command calculates their connectivity.
+Two triangles are "connected" if they have a single corner point in
+common or an edge in common (2 corner points).  Two line segments are
+"connected" if the they have an end point in common.  More technical
+details on connectivity and its significance for granular surface
+simulations is given on :doc:`Howto granular surfaces
+<Howto_granular_surfaces>` doc page.  In brief, a pair of connected
+surfaces interact with a particle which contacts both of them
+simultaneously according to a set of rules which are designed to
+generate physically sensible forces on the particle.
+
+Note that there is no requirement that all the surfaces be connected
+to one another.  The surfaces can represent the surface of one or more
+independent objects.  Particles in the specified group-ID interact
+with the surface when they are close enough to overlap (touch) one or
+more individual triangles or lines.  Both sides of a triangle or line
+interact with particles.  Thus a surface can be infinitely thin,
+e.g. the blade of a mixer.  See the :doc:`Howto granular surfaces
+<Howto_granular_surfaces>` doc page for restrictions on the geometry
+of a collection of triangles or lines.
+
+The nature of individual surface/particle interactions are determined
+by the *model* keyword.  Each use of the model keyword is applied to
+one or more particle types interacting with one or more surface types.
+The *ptype* argument is the particle type, *stype* is the surface
+type.
+
+Either *ptype* and *stype* can be specified as a single numeric value.
+Or a wildcard asterisk can be used to specify multiple particle or
+surface types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".
+If :math:`N` is the number of particle or surface types, then an
+asterisk with no numeric values means all types from 1 to :math:`N`.
+A leading asterisk means all types from 1 to n (inclusive).  A
+trailing asterisk means all types from n to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+The model keywords must specify an interactions for each particle type
+interacting with each surface type, otherwise an error is flagged.
+If use of the model keywords specifies an individual particle/surface
+type pair more than once, then the final specification is used.
+
+The number of particle types is the number of atom types in the
+system.  The number of surface types is determined by the maximum
+surface type in any of files read by the *input* keyword(s) or by the
+optional *smaxtype* keyword.  The latter can be useful if the
+:doc:`fix_modify type/region <fix_modify>` command (described below)
+is used to assign new types to surfaces after they are read in.  As
+for particles, there is no requirement that triangles/lines exist for
+every surface type.
+
+The *fstyle* argument (for force style) can be any of the styles
+defined by the :doc:`pair_style gran/\* <pair_gran>` or the more
+general :doc:`pair_style granular <pair_granular>` commands.
+Currently the options are *hooke*, *hooke/history*, or *hertz/history*
+for the former, and *granular* with all the possible options of the
+associated *pair_coeff* command for the latter.  The equation for the
+force between a triangle/line and a particle touching it is the same
+as the corresponding equation on the :doc:`pair_style gran/\*
+<pair_gran>` and :doc:`pair_style granular <pair_granular>` doc pages,
+in the limit of one of the two particles going to infinite radius and
+mass (flat surface).  Specifically, delta = radius - r = overlap of
+particle with triangle/line, m_eff = mass of particle, and the
+effective radius of contact = RiRj/Ri+Rj is set to the radius of the
+particle.
+
+The parameters *Kn*, *Kt*, *gamma_n*, *gamma_t*, *xmu*, *dampflag*,
+and the optional keyword *limit_damping* have the same meaning and
+units as those specified with the :doc:`pair_style gran/\*
+<pair_gran>` commands.  This means a NULL can be used for either *Kt*
+or *gamma_t* as described on that page.  If a NULL is used for *Kt*,
+then a default value is used where *Kt* = 2/7 *Kn*\ .  If a NULL is
+used for *gamma_t*, then a default value is used where *gamma_t* = 1/2
+*gamma_n*.
+
+Note that the fix surface/global command can be used multiple times
+though it is not typically necessary to do so.  Note that if it is
+used multiple times, the surfaces defined by the different commands
+will NOT be "connected" to each other in the manner described above or
+on the :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc
+page.
+
+----------
+
+These are the optional keywords and values.
+
+The *smax* keyword sets the maximum value *smaxtype* of a surface type
+which can be used.  By default, this is the maximum type of any
+surface defined by the *input* keyword(s).  If the :doc:`fix_modify
+type/region <fix_modify>` command (described below) will be used later
+to change a surface type to a larger value than the default, then the
+*smax* keyword can allow this.
+
+The *flat* keyword sets a *maxangle* threshold for the angle (in
+degrees) between two connected surfaces (triangles or line segments)
+which will be treated as "flat" by the particle/surface interaction
+models.  A flat connection means a single force will be applied to the
+particle even if it is contact with both surfaces simultaneously.  See
+the :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page
+for more details.  The default for *maxangle* is one degree.
+
+The *temperature* keyword is required if any of the granular models
+used includes a heat model which depends on the surface temperature.
+Otherwise it is ignored.  Its *Tsurf* value is the temperature of the
+surface in degrees Kelvin.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
+
+This fix defines two new keywords for the doc:`fix_modify
+<fix_modify>` command, *move* and *type/region*.  Because they are
+specific to this command, they are only described here, not on the
+doc:`fix_modify <fix_modify>` doc page.  Both keywords can be used
+multiple times.  In the description that follows, a surface means a
+triangle (3d) or line segment (2d).
+
+The *move* keyword can be used to make all or a subset of the surfaces
+move in a prescribed manner, similar to the :doc:`fix move <fix_move>`
+command.  The *type/region* keyword can be used to change the types of
+surfaces which are within a geometric region.  Their syntax is as follows:
+
+.. code-block:: LAMMPS
+
+   fix_modify fix-ID keyword values ...
+
+* fix-ID = ID of the fix to modify
+* keyword (specific to this fix) = *move* or *type/region*
+
+  .. parsed-literal::
+
+       *move* values = stype mstyle args
+          stype =  numeric surface type(s) (see comma-separated, asterisk form below)
+          mstyle = *none* or *linear* or *wiggle* or *rotate* or *transrot* or *variable*
+           *none* args = none
+           *linear* args = Vx Vy Vz
+           *wiggle* args = Ax Ay Az period
+           *rotate* args = Px Py Pz Rx Ry Rz period
+           *transrot* args = Vx Vy Vz Px Py Pz Rx Ry Rz period
+           *variable* args = v_dx v_dy v_dz v_vx v_vy v_vz
+       *type/region* values = stype region-ID
+         stype = numeric surface type
+         region-ID = ID of a region previously defined by the :doc:`region <region>` command
+
+The *stype* argument can specify one or more surface types.  It must
+specify all the surface types within a connecte object(s).  If an
+object is composed of surfaces of 2 or more types, it is an error to
+use the *move* keyword and not specify all those types, since this
+would break the connections.  Note that LAMMPS does NOT check that
+this requirement is met.  It is likewise an error to use the *move*
+keyword multiple times to induce motion which overlaps surfaces in
+ways that violate the surface geometry restrictions explained on the
+:doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page.
+Again, LAMMPS does NOT check that this requirement is met.
+
+The general format of *stype* is st,st,...,st where one or more *st*
+sub-arguments are separated by commas.  A single *st* sub-argument is
+either a single numeric value or contains a wildcard asterisk.  The
+asterisk is used in place of or in conjunction with numeric arguments
+to specify multiple type values.  This takes the form "\*" or "\*n" or
+"n\*" or "m\*n".  If :math:`N` is the number of atom types, then an
+asterisk with no numeric values means all types from 1 to :math:`N`.
+A leading asterisk means all types from 1 to n (inclusive).  A
+trailing asterisk means all types from n to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+The *mstyle* argument is one of the listed styles above.  The *none*
+style turns off motion which was previously enabled, e.g. stops the
+rotation of an object.  Again, the list of surface types must include
+all the surfaces in a connected object.  The other *move* styles and
+their effects on motion are the same as those defined by the :doc:`fix
+move <fix_move>` command.  Their arguments are also the same as those
+documented by the :doc:`fix move <fix_move>` command.
+
+The move *variable* style for this command is more limited than for
+the :doc:`fix move <fix_move>` command.  Only an equal-style variable
+can be used, as defined by the :doc:`variable <variable>`.  Atom-style
+variables cannot be used.  Also, if both the displacement and velocity
+variables for a particular x,y,z component are specified as NULL, then
+no change is made to those position or velococity components of an
+individual triangle/line, which is different than the explanation
+given by the :doc:`fix move <fix_move>` command for individual
+particles.
+
+Note that for *local* surfaces the same motion operations can be
+performed using the :doc:`fix move <fix_move>` command with a group-ID
+defined by the :doc:`group <group>` which includes the appropriate
+particle types for triangle and line-segment particles.
+
+The *type/region* keyword can be used to re-assign surface types to
+surfaces after they have been initialized by the *input* keyword.
+This is most useful for STL triangles since STL files do not allow for
+assignment of types to individual triangles.
+
+The *stype* argument is a single numeric value, which must be between
+1 and maxtype inclusive.  Maxtype is either the maximum type of all
+surfaces read in by the *input* keyword or the setting of the optional
+*smax* keyword.  The *region-ID* is the ID of a geometric region
+defined by the :doc:`region <region>` command.  Note that regions can
+be the inside or outside of a geometric object, such as a sphere or
+block.  The geometric center point of a triangle or line segment is
+used to determine where a surface is in the region or not.  If it is,
+its type is reset to *stype*.
+
+Examples for both keywords are as follows:
+
+.. code-block:: LAMMPS
+
+   fix_modify 1 move 2 rotate 0 0 0 0 0 1 25
+   fix_modify 1 move 1,3*5,8* rotate 0 0 0 0 0 1 25
+   fix_modify 1 type/region 3 myBlock
+
+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
+""""""""""""
+
+Molecule IDs are not currently used by granular surface interactions,
+though they may be in the future.  They are intended to be assigned
+uniquely to each inter-connected set of triangles/lines, as if each
+object were a "molecule".  However, this is not required, and LAMMPS
+does not check that this is the case.  LAMMPS will issue a warning if
+a set of inter-connected triangles/lines do not all have the same
+molecule ID, in case this was not intentional.
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix surface/local <fix_surface_local>`
+
+Default
+"""""""
+
+The keyword defaults are smax = max type of all surfaces defined by
+the input keyword(s), flat = one degree, temperaure = none.

doc/src/fix_surface_local.rst

@@ -0,0 +1,220 @@
+.. index:: fix surface/local
+
+fix surface/local command
+===============
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID surface/local input args input args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* surface/local = style name of this fix command
+* input = zero or more input keywords can be specified
+
+  .. parsed-literal::
+
+       *input* args = source source-args
+         *source* = *mol* or *stl*
+            *mol* arg = template-ID
+               template-ID = ID of molecule template specified in a
+               separate :doc:`molecule <molecule>` command, which defines a set of triangles or lines
+            *stl* args = stype stlfile
+               stype = numeric type assigned to all triangles in STL file
+               stlfile = STL filename which defines a set of triangles
+
+* zero or more keyword/value pairs may be appended
+* keyword = *flat*
+
+  .. parsed-literal::
+
+       *flat* value = maxangle
+         maxangle = maximum angle (degrees) between a pair of connected triangles/lines for a flat connection
+
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   read_data data.tris
+   fix 1 all surface/local NULL
+
+   molecule tris surf.tri
+   fix 1 all surface/local tris
+
+   fix 1 all surface/local surf.tri.stl
+
+Description
+"""""""""""
+
+Enable granular surfaces to be used as boundary conditions on
+particles in a granular simulation.  Granular surfaces are defined as
+a set of triangles (for 3d models) or a set of line segments (for 2d
+models).
+
+The :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page
+gives an overview of granular surfaces of two types, *global* and
+*local*, and gives guidelines for how they should be defined.
+
+This command is used for models with *local* surfaces.  The :doc:`fix
+surface/global <fix_surface_global>` command is used for models with
+*global* surfaces.  As explained on the :doc:`Howto granular surfaces
+<Howto_granular_surfaces>` doc page, *local* surfaces are most
+appropriate when there is a large number of them.  They should
+typically use surfaces (triangles/lines) whose size is no more than a
+few times larger than the spherical particles used in a granular
+model.  There can be as many surfaces as needed to describe one or
+more physical surfaces at high resolution.
+
+*Local* triangles or line segments are stored as triangle or line
+particles and are distributed across processors in the same manner as
+other particles, based on which processor's sub-domain the center of
+the triangle or line segment is inside of.
+
+*Local* triangles/lines can be defined in 3 ways.  The latter two
+correspond to the 2 options listed above for the *source* argument of
+the *input* keyword:
+
+* via a data file, read by the :doc:`read_data <read_data>` command
+* via a molecule file(s), read by the :doc:`molecule <molecule>` command
+* via an STL file(s), read by this commmand
+
+If triangles/lines were previously read in by the :doc:`read_data
+<read_data>` command, then distributed triangles or lines already
+exist.  As explained on the :doc:`Howto granular surfaces
+<Howto_granular_surfaces>` doc page, these are "particles" as defined
+by the :doc:`atom_style tri or line <atom_style>` command, typically
+as a sub-style of the :doc:`atom_style hybrid <atom_style>` command.
+
+Use of the *input* keyword adds new triangle/line particles to the
+system.
+
+If triangles or lines were previously read in by the :doc:`molecule
+<molecule>` command, the *source* keyword of the *input* keyword is
+*mol* and tts *template-ID* argument is the molecule template ID used
+with the :doc:`molecule <molecule>` command.  Note that a
+doc:`molecule <molecule>` command can read and assign serveral
+molecule files to the same template-ID.  Each molecule file must
+define triangles or lines, not atoms.  For multiple molecule files,
+the set of triangle or line particles defined by this input option
+will be the union of the triangles and lines from all the molecule
+files.  Note that each line/triangle in a molecule file is assigned a
+type and molecule ID.
+
+An STL (stereolithography) file defines a set of triangles.  For use
+with this command, the *source* argument of the *input* keyword is
+*stl*.  The *stype* argument is the numeric type assigned to all the
+triangles from the file.  Note that STL files do not contain types or
+other flags for each triangle.  The *stlfile* argument is the name of
+the STL file.  It can be in text or binary format; this command
+auto-detects the format. One triangle particle is created for each
+triangle in the STL file(s).  Note that STL files cannot be used for
+2d simulations since they only define triangles.  Each triangle
+partilce from an STL file is assigned a molecule ID = 1.
+
+This `Wikepedia page
+<https://en.wikipedia.org/wiki/STL_(file_format)>`_ describes the
+format of both text and binary STL files.  Binary STL files can be
+converted to ASCII for editing with the stl_bin2txt tool in the
+lammps/tools directory.  Examples of text STL files are included in
+the examples/gransurf directory.
+
+Note that this command allows for pre-defined triangle/line particles
+read in by the :doc:`read_data <read_data>` command as well as ultiple
+uses of the *input* keyword, each with a *source* argument as either
+*mol* or *stl*.  The number of triangle/line particles created by this
+command will be the union of those already read by the :doc:`read_data
+<read_data>` command and those specified by the *input* keywords.
+
+Once all the distributed triangle/line particles are defined, this
+command calculates their connectivity.  Two triangles are "connected"
+if they have a single corner point in common or an edge in common (2
+corner points).  Two line segments are "connected" if the they have an
+end point in common.  More technical details on connectivity and its
+significance for granular surface simulations is given on :doc:`Howto
+granular surfaces <Howto_granular_surfaces>` doc page.  In brief, a
+pair of connected surfaces interact with a particle which contacts
+both of them simultaneously according to a set of rules which are
+designed to generate physically sensible forces on the particle.
+
+Note that there is no requirement that all the surfaces be connected
+to one another.  The surfaces can represent the surface of one or more
+independent objects.  Particles interact with the surface when they
+are close enough to overlap (touch) one or more individual triangles
+or lines.  Both sides of a triangle or line interact with particles.
+Thus a surface can be infinitely thin, e.g. the blade of a mixer.  See
+the :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page
+for restrictions on the geometry of a collection of triangles or
+lines.
+
+The nature of individual surface/particle interactions are determined
+by the :doc:`pair_coeff <pair_coeff>` command which specifies
+interaction parameeters for each pair of particle types.  It is thus
+important to specify different types for granular particles and
+granular surfaces (triangle/line particles).  Typically a granular
+simulation with local surfaces uses the :doc:`pair_style hybrid
+<pair_hybrid>` command so that multiple sub-styles can be defined by
+the :doc:`pair_coeff <pair_coeff>` command, one or more for
+particle/particle interactions, and one or more for particle/surface
+interactions.  Similar to the :doc:`fix surface/global
+<fix_surface_global>` command this allows multiple particle/surface
+granular interaction models to be used, based on the surface particle
+types.
+
+----------
+
+These are the optional keywords and values.
+
+The *flat* keyword sets a *maxangle* threshold for the angle (in
+degrees) between two connected surfaces (triangles or line segments)
+which will be treated as "flat" by the particle/surface interaction
+models.  A flat connection means a single force will be applied to the
+particle even if it is contact with both surfaces simultaneously.  See
+the :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc page
+for more details.  The default for *maxangle* is one degree.
+
+The *temperature* keyword is required if any of the granular models
+defined by the :doc:`pair_coeff <pair_coeff>` command includes a heat
+model which depends on the surface temperature.  Otherwise it is
+ignored.  Its *Tsurf* value is the temperature of the surface in
+degrees Kelvin.
+
+Note that the *temperature* keyword used by the :doc:`fix
+surface/global <fix_surface_global>` command is not used by this
+command.  This is because the particle/surf interactions are computed
+by pair styles and that is where the temperature is applicable.
+
+Note that the *smax* keyword used by the :doc:`fix surface/global
+<fix_surface_global>` command is not used by this command.  This is
+because local triangles and lines are already particles and their type
+is limited by the maximum number of particle types.
+
+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
+""""""""""""
+
+none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix surface/global <fix_surface_global>`
+
+Default
+"""""""
+
+none

doc/src/group.rst

@@ -112,7 +112,9 @@ to a group.
 The *region* style puts all atoms in the region volume into the group.
 Note that this is a static one-time assignment.  The atoms remain
 assigned (or not assigned) to the group even in they later move out of
-the region volume.
+the region volume.  For extended triangle or line-segment particle,
+the center point of the triangle or line-segment is used to determine
+whether the particle is in the region or not.
 
 The *type*, *id*, and *molecule* styles put all atoms with the
 specified atom types, atom IDs, or molecule IDs into the group.  These

doc/src/molecule.rst

@@ -64,6 +64,16 @@ templates include:
 * :doc:`create_atoms <create_atoms>`
 * :doc:`atom_style template <atom_style>`
 
+It can also be used to define a collection of line segments (2d) or
+triangles (3d) which define an object's surface or a boundary
+condition for granular particles to interact with, via these commands:
+
+* :doc:`fix surface/global <fix_surface_global>`
+* :doc:`fix surface/local <fix_surface_local>`
+
+See the :doc:`Howto granular surfaces <Howto_granular_surfaces>` doc
+page for more details on these kinds of models.
+
 The ID of a molecule template can only contain alphanumeric characters
 and underscores.
 
@@ -95,6 +105,11 @@ use that attribute (e.g. no bonds).
    labels will determine the actual types directly depending on the
    current :doc:`labelmap <labelmap>` settings.
 
+   .. note::
+
+   For molecule files defining line segments or triangles, only the
+   *toff* keyword is relevant; the other offset keywords are ignored.
+
 The *scale* keyword scales the size of the molecule.  This can be
 useful for modeling polydisperse granular rigid bodies.  The scale
 factor is applied to each of these properties in the molecule file, if
@@ -105,21 +120,26 @@ mass of the molecule (header keyword = mass), the center-of-mass of
 the molecule (header keyword = com), and the moments of inertia of the
 molecule (header keyword = inertia).
 
+   .. note::
+
+   For molecule files defining line segments or triangles, the *scale*
+   keyword is ignored.
+
 .. note::
 
    The molecule command can be used to define molecules with bonds,
    angles, dihedrals, impropers, or special bond lists of neighbors
-   within a molecular topology, so that you can later add the molecules
-   to your simulation, via one or more of the commands listed above.
-   Since this topology-related information requires that suitable storage
-   is reserved when LAMMPS creates the simulation box (e.g. when using
-   the :doc:`create_box <create_box>` command or the
-   :doc:`read_data <read_data>` command) suitable space has to be reserved
-   so you do not overflow those pre-allocated data structures when adding
-   molecules later.  Both the :doc:`create_box <create_box>` command and
-   the :doc:`read_data <read_data>` command have "extra" options which
-   ensure space is allocated for storing topology info for molecules that
-   are added later.
+   within a molecular topology, so that you can later add the
+   molecules to your simulation, via one or more of the commands
+   listed above.  Since this topology-related information requires
+   that suitable storage is reserved when LAMMPS creates the
+   simulation box (e.g. when using the :doc:`create_box <create_box>`
+   command or the :doc:`read_data <read_data>` command) suitable space
+   has to be reserved so you do not overflow those pre-allocated data
+   structures when adding molecules later.  Both the :doc:`create_box
+   <create_box>` command and the :doc:`read_data <read_data>` command
+   have "extra" options which ensure space is allocated for storing
+   topology info for molecules that are added later.
 
 ----------
 
@@ -166,18 +186,18 @@ commands.  Here is a simple example for a TIP3P water molecule:
 
    1   1      2      1      3
 
-A molecule file has a header and a body.  The header appears first.  The
-first line of the header and thus of the molecule file is *always*
+A molecule file has a header and a body.  The header appears first.
+The first line of the header and thus of the molecule file is *always*
 skipped; it typically contains a description of the file or a comment
 from the software that created the file.
 
 Then lines are read one line at a time.  Lines can have a trailing
-comment starting with '#' that is ignored.  There *must* be at least one
-blank between any valid content and the comment.  If the line is blank
-(i.e. contains only white-space after comments are deleted), it is
-skipped.  If the line contains a header keyword, the corresponding
-value(s) is/are read from the line.  A line that is *not* blank and does
-*not* contains a header keyword begins the body of the file.
+comment starting with '#' that is ignored.  There *must* be at least
+one blank between any valid content and the comment.  If the line is
+blank (i.e. contains only white-space after comments are deleted), it
+is skipped.  If the line contains a header keyword, the corresponding
+value(s) is/are read from the line.  A line that is *not* blank and
+does *not* contains a header keyword begins the body of the file.
 
 The body of the file contains zero or more sections.  The first line
 of a section has only a keyword.  The next line is skipped.  The
@@ -192,7 +212,8 @@ line.  The keyword should appear at the end of the line.  All these
 settings have default values, as explained below.  A line need only
 appear if the value(s) are different than the default, except when
 defining a *body* particle, which requires setting the number of
-*atoms* to 1, and setting the *inertia* in a specific section (see below).
+*atoms* to 1, and setting the *inertia* in a specific section (see
+below).
 
 .. list-table::
       :header-rows: 1
@@ -242,6 +263,18 @@ defining a *body* particle, which requires setting the number of
         - inertia
         - 6 components of inertia tensor of molecule
         - computed
+      * - Nlines
+        - lines
+        - # of lines Nlines in molecule
+        - 0
+      * - Ntris
+        - triangles
+        - # of triangle Ntris in molecule
+        - 0
+
+A molecule file can contain only either the *atoms*, *lines*, or
+*triangles* keyword.  All the other keywords can only be used for
+a molecule file containing the *atoms* keyword.
 
 For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
 this quantity itself if needed, assuming the molecules consist of a set
@@ -266,6 +299,11 @@ These are the allowed section keywords for the body of the file.
 * *Special Bond Counts, Special Bonds* = special neighbor info
 * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
 * *Body Integers, Body Doubles* = body-property sections
+* *Lines, Triangles* = corner points of lines or triangles
+
+Similar to the corresponding keywords, a molecule file can only
+contain either a Coords, Lines, or Triangles section.  All of the
+other sections can only be used in molecule files for atoms.
 
 For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
 atom/bond/angle/etc type can be specified either as a number (numeric
@@ -669,6 +707,68 @@ the file format.
 
 ----------
 
+*Lines* section:
+
+* one line per line segment
+* line syntax: ID molecule-ID type x1 y1 x2 y2
+* molecule-ID = molecule-ID of the line segment
+* type = type of the line segment
+* x1,y1,x2,y2 = coords of two endpoints of line segment
+
+Each line segment is assigned a molecule-ID and type, similar to an
+atom type.  This allows a collection of lines to represent multiple 2d
+bodies, e.g. a collection of squares.  Line-segments in each could
+have a different molecule-ID, or the left-facing edges could have a
+unique atom type.
+
+The coords of two different line segments which are connected by a
+common point should list the exact same coordinates for the common
+point.  This allows a command like :doc:`fix surface/local
+<fix_surface_local>` to infer connectivity of the two line segments.
+
+The ordering of the two points defines the direction of an outward
+normal for the line segment.  This is defined by a right-hand rule.
+The outward normal N = (0,0,1) x (p2-p1), where p1 and p2 are the 2
+points.  In other words, a unit z-direction vector is crossed into the
+vector from p1 to p2 to determine the normal.
+
+It depends on how the line segments are used by other commands in
+LAMMPS whether the normal direction matters or not.
+
+----------
+
+*Triangles* section:
+
+* one line per triangle
+* line syntax: ID molecule-ID type x1 y1 z1 x2 y2 z2 x3 y3 z3
+* molecule-ID = molecule-ID assigned triangle
+* type = type assigned to triangle
+* x1,y1,z1,x2,y2,z2,x3,y3,z3 = coords of three corner points of triangle
+
+Each triangle is assigned a molecule-ID and type, similar to an atom
+type.  This allows a collection of triangles to represent multiple 3d
+objects, e.g. a curved surface on the left and right of the simulation
+box.  Triangles in each could have a different molecule-ID, or the the
+triangles in the upper half could have a different type than those in
+the lower half.
+
+The coords of two different triangles which share a common edge (2
+points) or corner point (single point) should list the exact same
+coordinates for the common points.  This allows a command like
+:doc:`fix surface/local <fix_surface_local>` to infer connectivity of
+the two triangles.
+
+The ordering of the three points defines the direction of the outward
+normal for the triangle. This is defined by a right-hand rule.  The
+outward normal N = (p2-p1) x (p3-p1), where p1, p2, p3 are the 3
+point.  In other words, the edge from p1 to p2 is crossed into the
+edge from p1 to p3 to determine the normal.
+
+It depends on how the triangles are used by other commands in LAMMPS
+whether the normal direction matters or not.
+
+----------
+
 Restrictions
 """"""""""""
 

examples/gransurf/data.line

@@ -0,0 +1,32 @@
+LAMMPS data file for line box
+
+9 atoms
+9 lines
+2 atom types
+-15 15 xlo xhi
+-15 15 ylo yhi
+-0.5 0.5 zlo zhi
+
+Atoms
+
+1 1 2 1 1 8.5 5 0
+2 1 2 1 1 5 8.5 0
+3 1 2 1 1 -5 8.5 0
+4 1 2 1 1 -8.5 5 0
+5 1 2 1 1 -8.5 -5 0
+6 1 2 1 1 -5 -10 0
+7 1 2 1 1 5 -10 0
+8 1 2 1 1 10 -5 0 
+9 1 2 1 1 0 -6.95 0
+
+Lines
+
+1 7 0 10 10
+2 10 10 0 7
+3 0 7 -10 10
+4 -10 10 -7 0
+5 -7 0 -10 -10
+6 -10 -10 0 -10
+7 0 -10 10 -10
+8 10 -10 10 0
+9 0 -9.9 0 -4

examples/gransurf/data.tri

@@ -0,0 +1,22 @@
+LAMMPS data file for tri box
+
+4 atoms
+4 triangles
+2 atom types
+-7.0 7.0 xlo xhi
+-7.0 7.0 ylo yhi
+0.0 9.0 zlo zhi
+
+Atoms
+
+1 1 2 1 1 0 -4 0
+2 1 2 1 1 4 0 0
+3 1 2 1 1 0 4 0
+4 1 2 1 1 -4 0 0
+
+Triangles
+
+1 -6 -6 0 6 -6 0 0 0 0
+2 6 -6 0 6 6 0 0 0 0
+3 6 6 0 -6 6 0 0 0 0
+4 -6 -6 0 0 0 0 -6 6 0

examples/gransurf/data.tribox

@@ -0,0 +1,62 @@
+LAMMPS data file generated from box24.stl
+
+24 atoms
+24 triangles
+2 atom types
+-9.0 9.0 xlo xhi
+-9.0 9.0 ylo yhi
+-9.0 9.0 zlo zhi
+
+Atoms
+
+1 1 2 1 1 4.0 0.0 -6.0
+2 1 2 1 1 4.0 0.0 6.0
+3 1 2 1 1 0.0 -4.0 6.0
+4 1 2 1 1 -4.0 0.0 6.0
+5 1 2 1 1 0.0 -4.0 -6.0
+6 1 2 1 1 -4.0 0.0 -6.0
+7 1 2 1 1 0.0 4.0 6.0
+8 1 2 1 1 0.0 4.0 -6.0
+9 1 2 1 1 4.0 6.0 0.0
+10 1 2 1 1 0.0 6.0 4.0
+11 1 2 1 1 4.0 -6.0 0.0
+12 1 2 1 1 0.0 -6.0 4.0
+13 1 2 1 1 0.0 6.0 -4.0
+14 1 2 1 1 -4.0 6.0 0.0
+15 1 2 1 1 0.0 -6.0 -4.0
+16 1 2 1 1 -4.0 -6.0 0.0
+17 1 2 1 1 6.0 4.0 0.0
+18 1 2 1 1 6.0 0.0 -4.0
+19 1 2 1 1 -6.0 4.0 0.0
+20 1 2 1 1 -6.0 0.0 -4.0
+21 1 2 1 1 6.0 0.0 4.0
+22 1 2 1 1 6.0 -4.0 0.0
+23 1 2 1 1 -6.0 0.0 4.0
+24 1 2 1 1 -6.0 -4.0 0.0
+
+Triangles
+
+1 0.0 0.0 -6.0 6.0 6.0 -6.0 6.0 -6.0 -6.0
+2 0.0 0.0 6.0 6.0 -6.0 6.0 6.0 6.0 6.0
+3 0.0 0.0 6.0 -6.0 -6.0 6.0 6.0 -6.0 6.0
+4 -6.0 6.0 6.0 -6.0 -6.0 6.0 0.0 0.0 6.0
+5 -6.0 -6.0 -6.0 0.0 0.0 -6.0 6.0 -6.0 -6.0
+6 0.0 0.0 -6.0 -6.0 -6.0 -6.0 -6.0 6.0 -6.0
+7 0.0 0.0 6.0 6.0 6.0 6.0 -6.0 6.0 6.0
+8 6.0 6.0 -6.0 0.0 0.0 -6.0 -6.0 6.0 -6.0
+9 6.0 6.0 -6.0 0.0 6.0 0.0 6.0 6.0 6.0
+10 0.0 6.0 0.0 -6.0 6.0 6.0 6.0 6.0 6.0
+11 6.0 -6.0 6.0 0.0 -6.0 0.0 6.0 -6.0 -6.0
+12 0.0 -6.0 0.0 6.0 -6.0 6.0 -6.0 -6.0 6.0
+13 0.0 6.0 0.0 6.0 6.0 -6.0 -6.0 6.0 -6.0
+14 -6.0 6.0 6.0 0.0 6.0 0.0 -6.0 6.0 -6.0
+15 0.0 -6.0 0.0 -6.0 -6.0 -6.0 6.0 -6.0 -6.0
+16 0.0 -6.0 0.0 -6.0 -6.0 6.0 -6.0 -6.0 -6.0
+17 6.0 6.0 6.0 6.0 0.0 0.0 6.0 6.0 -6.0
+18 6.0 0.0 0.0 6.0 -6.0 -6.0 6.0 6.0 -6.0
+19 -6.0 6.0 -6.0 -6.0 0.0 0.0 -6.0 6.0 6.0
+20 -6.0 0.0 0.0 -6.0 6.0 -6.0 -6.0 -6.0 -6.0
+21 6.0 0.0 0.0 6.0 6.0 6.0 6.0 -6.0 6.0
+22 6.0 -6.0 -6.0 6.0 0.0 0.0 6.0 -6.0 6.0
+23 -6.0 0.0 0.0 -6.0 -6.0 6.0 -6.0 6.0 6.0
+24 -6.0 0.0 0.0 -6.0 -6.0 -6.0 -6.0 -6.0 6.0

examples/gransurf/in.line.gran.data

@@ -0,0 +1,59 @@
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+read_data	data.line
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           line type 2
+
+fix             fsl all surface/local
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run             10000

examples/gransurf/in.line.gran.global

@@ -0,0 +1,59 @@
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+molecule        lines surf.line
+
+fix             20 all surface/global input mol lines &
+                model * * hooke 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global lines hooke/history &
+#                4000.0 NULL 100.0 NULL 0.5 1
+
+# rotate the box
+
+fix_modify      20 move * rotate 0 0 0 0 0 1 25
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 -1 0
+#fix             4 all viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+#fix             ins all pour 100 1 4767548 vol 0.4 10 &
+#	        diam one 1.0 region slab
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.6 adiam 1.0 fix 20 type 0.5 0.0
+dump_modify	2 pad 5
+
+run	        10000

examples/gransurf/in.line.gran.surf

@@ -0,0 +1,61 @@
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+
+molecule        lines surf.line
+fix             20 all surface/local input mol lines
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           line type 2
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run	       10000

examples/gransurf/in.tri.gran.data

@@ -0,0 +1,64 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tri
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+fix             fsl all surface/local
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000

examples/gransurf/in.tri.gran.global

@@ -0,0 +1,62 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tri
+
+fix             20 all surface/global input mol tris &
+                model * * hooke 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history &
+#                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+#fix             ins all pour 100 1 4767548 vol 0.4 10 &
+#	        diam one 1.0 region slab ignore
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+dump_modify	2 pad 5
+
+run	        5000
+
+fix_modify      20 move * rotate 0 0 0 0 0 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000

examples/gransurf/in.tri.gran.global.stl

@@ -0,0 +1,60 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global input stl 2 surf.tri.stl &
+                model * * hooke 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global surf.tri.stl hooke/history &
+#                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+#fix             ins all pour 100 1 4767548 vol 0.4 10 &
+#	        diam one 1.0 region slab ignore
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+dump_modify	2 pad 5
+
+run	        5000
+
+fix_modify      20 move * rotate 0 0 0 0 0 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000

examples/gransurf/in.tri.gran.surf

@@ -0,0 +1,66 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+
+molecule        tris surf.tri
+fix             20 all surface/local input mol tris
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000

examples/gransurf/in.tri.gran.surf.stl

@@ -0,0 +1,65 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+
+fix             20 all surface/local input stl 2 surf.tri.stl
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1 &
+                zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000

examples/gransurf/in.tribox.gran.data

@@ -0,0 +1,70 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tribox
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+fix             fsl all surface/local
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+

examples/gransurf/in.tribox.gran.global

@@ -0,0 +1,65 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tribox
+
+fix             20 all surface/global input mol tris &
+                model * * hooke 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history &
+#                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+#fix             ins all pour 100 1 4767548 vol 0.4 10 &
+#	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+dump_modify	2 pad 5
+
+run	        5000
+
+fix_modify      20 move * rotate 0 0 0 0 0 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000
+
+fix_modify      20 move * rotate 0 0 0 1 1 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000

examples/gransurf/in.tribox.gran.global.stl

@@ -0,0 +1,63 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global input stl 2 surf.tri.stl &
+                model * * hooke 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global surf.tribox.stl hooke/history &
+#                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+#fix             ins all pour 100 1 4767548 vol 0.4 10 &
+#	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+dump_modify	2 pad 5
+
+run	        5000
+
+fix_modify      20 move * rotate 0 0 0 0 0 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000
+
+fix_modify      20 move * rotate 0 0 0 1 1 1 25
+run	        5000
+
+fix_modify      20 move * none
+run             5000

examples/gransurf/in.tribox.gran.surf

@@ -0,0 +1,72 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+molecule        tris surf.tribox
+fix             20 all surface/local input mol tris
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+

examples/gransurf/in.tribox.gran.surf.stl

@@ -0,0 +1,71 @@
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+fix             20 all surface/local input stl 2 surf.tribox.stl
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 &
+                tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+group           tri type 2
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 &
+	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type &
+		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+
+unfix           1
+set             group tri angmom 0.0 0.0 0.0
+velocity        tri set 0.0 0.0 0.0
+run             5000
+

examples/gransurf/log.1Jul24.line.gran.data.g++.1

@@ -0,0 +1,246 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+read_data	data.line
+Reading data file ...
+  orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  9 atoms
+  9 lines
+  read_data CPU = 0.001 seconds
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           line type 2
+9 atoms in group line
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 6.0201533
+  ghost atom cutoff = 6.0201533
+  binsize = 3.0100766, bins = 10 10 1
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair line/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.08 | 12.08 | 12.08 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           9   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          16   19.603933      1.0483784      0.66213376     0.32673222   
+       200          16   19.831299      1.6167923      1.0211319      0.33052165   
+       300          16   20.119751      2.3379224      1.4765825      0.33532918   
+       400          16   20.469289      3.2117688      2.0284855      0.34115482   
+       500          16   20.879914      4.2383315      2.676841       0.34799857   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          27   12.449543      2.1129055      1.3869354      0.35243867   
+       700          27   12.770891      2.6043792      1.7214254      0.38349742   
+       800          27   12.943117      2.8677827      1.9147069      0.37516936   
+       900          27   13.109917      3.1228891      2.1263001      0.38019376   
+      1000          27   12.990208      2.9398046      2.0739419      0.42599315   
+      1100          27   12.719767      2.5261889      1.8187978      0.45457071   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          35   9.8597994      1.8985781      1.2816098      0.38022839   
+      1300          35   9.7545391      1.7554241      1.2048448      0.37276257   
+      1400          35   9.7769878      1.7859543      1.2306073      0.37760148   
+      1500          35   9.9443391      2.013552       1.3984072      0.38116488   
+      1600          35   10.108938      2.2374064      1.548047       0.38622523   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          45   8.2127721      2.1026641      1.4164548      0.41493848   
+      1800          45   8.3070246      2.221153       1.4818344      0.48996397   
+      1900          45   8.3176349      2.2344917      1.4850053      0.47813979   
+      2000          45   8.2600241      2.1620667      1.4483974      0.43264606   
+      2100          45   8.1701045      2.0490249      1.3718091      0.42642557   
+      2200          45   8.1506342      2.0245479      1.3453729      0.41836911   
+      2300          57   6.4845955      1.6035877      1.0816884      0.47342846   
+      2400          57   6.4586802      1.5727098      1.0558623      0.46664067   
+      2500          57   6.4961252      1.6173252      1.0834364      0.44274885   
+      2600          57   6.6039251      1.7457676      1.176221       0.41973624   
+      2700          57   6.5554483      1.688008       1.1497303      0.44701076   
+      2800          57   6.5567541      1.6895638      1.1752899      0.43024349   
+      2900          69   5.8154825      1.8251539      1.249261       0.48033376   
+      3000          69   6.0391782      2.0829727      1.4327472      0.47214476   
+      3100          69   6.1705005      2.2343272      1.5419433      0.48474059   
+      3200          69   6.132184       2.1901659      1.4819192      0.55938449   
+      3300          69   5.8754263      1.8942417      1.2793954      0.49963347   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          76   5.2906822      1.6520066      1.1205016      0.45528549   
+      3500          76   5.3445576      1.7132287      1.1601016      0.47797559   
+      3600          76   5.4367165      1.8179547      1.2411665      0.48683301   
+      3700          76   5.4872464      1.875375       1.273533       0.498041     
+      3800          76   5.4740601      1.8603906      1.266449       0.48678074   
+      3900          76   5.1850894      1.5320148      1.0615263      0.54254269   
+      4000          88   4.6518362      1.4992438      1.0244353      0.4970414    
+      4100          88   4.7393433      1.596848       1.1075633      0.5183373    
+      4200          88   4.5210383      1.3533539      0.95365012     0.45549812   
+      4300          88   4.7560439      1.6154755      1.0954535      0.50256618   
+      4400          88   4.9238859      1.8026839      1.219188       0.55797132   
+      4500          88   4.9156862      1.7935381      1.225359       0.55455375   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          96   4.553808       1.6842213      1.1456065      0.49939928   
+      4700          96   4.6015699      1.7369816      1.1986257      0.4988626    
+      4800          96   4.6404333      1.7799121      1.2251247      0.55167427   
+      4900          96   4.7241213      1.872358       1.2735481      0.71833717   
+      5000          96   4.7796445      1.9336918      1.3156784      0.66606358   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      5100         104   4.5227739      1.894436       1.2925792      0.68747814   
+      5200         104   4.5828         1.9602093      1.3495676      0.72748168   
+      5300         104   4.2544924      1.600468       1.1051773      0.60419007   
+      5400         104   4.3514327      1.7066898      1.1556029      0.64443629   
+      5500         104   4.3561805      1.7118922      1.1567283      0.64063026   
+      5600         104   4.4135092      1.7747098      1.2134595      0.64422908   
+      5700         109   4.1731736      1.6457981      1.1165517      0.62979315   
+      5800         109   4.2360976      1.7144426      1.1586539      0.59262337   
+      5900         109   4.3212416      1.8073269      1.2143855      0.63775197   
+      6000         109   4.4240471      1.9194784      1.2958061      0.60804743   
+      6100         109   4.5373715      2.043105       1.3752433      0.63992905   
+      6200         109   4.4471074      1.9446351      1.3287311      0.69275635   
+      6300         109   4.4126755      1.9070729      1.3022258      0.62040671   
+      6400         109   4.5165479      2.0203883      1.3863072      0.63682236   
+      6500         109   4.2755226      1.7574517      1.2024768      0.61086932   
+      6600         109   4.1690976      1.6413517      1.1235094      0.5863121    
+      6700         109   4.0973952      1.5631308      1.0585691      0.64655034   
+      6800         109   4.106546       1.5731135      1.0593334      0.59742247   
+      6900         109   4.09205        1.5572998      1.0468541      0.54449389   
+      7000         109   4.1494965      1.6199687      1.0886876      0.58703636   
+      7100         109   4.220005       1.696887       1.1346313      0.58309534   
+      7200         109   4.2559993      1.7361535      1.1633567      0.59963725   
+      7300         109   4.3570648      1.8464068      1.2394663      0.59299795   
+      7400         109   4.5559427      2.0633645      1.3860772      0.5985101    
+      7500         109   4.7538736      2.2792891      1.5322837      0.60614702   
+      7600         109   4.9145244      2.4545446      1.6536668      0.63147745   
+      7700         109   5.0299608      2.5804752      1.757645       0.69057802   
+      7800         109   5.3520062      2.9317973      2.000564       0.66812054   
+      7900         109   5.4070924      2.9918914      2.0567247      0.7668346    
+      8000         109   4.9680652      2.5129527      1.7229154      0.65816251   
+      8100         108   4.8654372      2.3758475      1.6345121      0.6217302    
+      8200         108   4.9502871      2.4684897      1.6821321      0.67733955   
+      8300         106   5.1164153      2.5984884      1.7604625      0.65703214   
+      8400         104   5.1073874      2.5350232      1.7227477      0.61775984   
+      8500         103   5.1173391      2.518278       1.7205254      0.63856204   
+      8600         101   4.9892171      2.3203624      1.5725655      0.66092676   
+      8700         101   4.9544942      2.2822054      1.5445523      0.63575204   
+      8800          98   4.7811294      2.0000094      1.360531       0.59490375   
+      8900          98   4.5866354      1.7856239      1.2179755      0.5479866    
+      9000          97   4.5098376      1.668686       1.1480979      0.51766609   
+      9100          96   4.4900228      1.6137609      1.1001152      0.58261959   
+      9200          96   4.5323564      1.6605248      1.1250204      0.52446222   
+      9300          96   4.6268095      1.7648625      1.1909651      0.51122536   
+      9400          94   4.6951589      1.7723935      1.2009448      0.51084023   
+      9500          94   4.7977809      1.8860106      1.2743862      0.55202711   
+      9600          92   4.9195403      1.9501151      1.3186129      0.52289861   
+      9700          92   5.0437791      2.0879899      1.4123366      0.69726187   
+      9800          92   4.9557322      1.9902793      1.3693209      0.63183721   
+      9900          92   5.0579303      2.1036943      1.4503547      0.5525547    
+     10000          92   4.9127294      1.9425566      1.3361772      0.54682786   
+Loop time of 0.370625 on 1 procs for 10000 steps with 92 atoms
+
+Performance: 11655971.193 tau/day, 26981.415 timesteps/s, 2.482 Matom-step/s
+88.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031333   | 0.031333   | 0.031333   |   0.0 |  8.45
+Neigh   | 0.02915    | 0.02915    | 0.02915    |   0.0 |  7.87
+Comm    | 0.0011333  | 0.0011333  | 0.0011333  |   0.0 |  0.31
+Output  | 0.29072    | 0.29072    | 0.29072    |   0.0 | 78.44
+Modify  | 0.015871   | 0.015871   | 0.015871   |   0.0 |  4.28
+Other   |            | 0.002418   |            |       |  0.65
+
+Nlocal:             92 ave          92 max          92 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 1464
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.line.gran.data.g++.4

@@ -0,0 +1,248 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+read_data	data.line
+Reading data file ...
+  orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  9 atoms
+  9 lines
+  read_data CPU = 0.001 seconds
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           line type 2
+9 atoms in group line
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 6.0201533
+  ghost atom cutoff = 6.0201533
+  binsize = 3.0100766, bins = 10 10 1
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair line/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           9   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          16   19.603933      1.0483784      0.66213376     0.32673222   
+       200          16   19.831299      1.6167923      1.0211319      0.33052165   
+       300          16   20.119751      2.3379224      1.4765825      0.33532918   
+       400          16   20.469289      3.2117688      2.0284855      0.34115482   
+       500          16   20.879914      4.2383315      2.676841       0.34799857   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          27   12.449543      2.1129055      1.3869354      0.35243867   
+       700          27   12.770891      2.6043792      1.7214254      0.38349742   
+       800          27   12.943117      2.8677827      1.9147069      0.37516936   
+       900          27   13.108843      3.121247       2.1253115      0.38032946   
+      1000          27   12.984928      2.9317288      2.0698845      0.41762763   
+      1100          27   12.721952      2.5295302      1.8183899      0.45463442   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          35   9.8620936      1.9016982      1.2818983      0.38031565   
+      1300          35   9.7562992      1.7578179      1.2054393      0.37155987   
+      1400          35   9.7634141      1.7674941      1.2257167      0.40489503   
+      1500          35   9.9265493      1.9893579      1.3730689      0.44243147   
+      1600          35   10.124257      2.2582409      1.5638344      0.3881931    
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          45   8.17872        2.0598558      1.4054749      0.40405845   
+      1800          45   8.3495746      2.2746444      1.5611373      0.4161154    
+      1900          45   8.3549118      2.281354       1.5264615      0.58558494   
+      2000          45   8.466023       2.4210367      1.6128843      0.43527142   
+      2100          45   8.3019659      2.2147934      1.4788849      0.40709585   
+      2200          45   8.3935397      2.3299148      1.5526831      0.42713391   
+      2300          57   6.6026997      1.7443076      1.1713462      0.44233027   
+      2400          57   6.5994805      1.7404719      1.1751702      0.43246067   
+      2500          57   6.5640783      1.6982905      1.1368997      0.46168872   
+      2600          57   6.6039644      1.7458144      1.1747368      0.43261873   
+      2700          57   6.4602492      1.5745793      1.0736669      0.44103997   
+      2800          57   6.5736746      1.7097244      1.1669705      0.42453827   
+      2900          69   5.8037651      1.8116491      1.2327379      0.45474569   
+      3000          69   6.0851724      2.135983       1.4490384      0.4768338    
+      3100          69   6.2646568      2.3428464      1.5760684      0.59595364   
+      3200          69   6.1537104      2.2149759      1.4941616      0.5329903    
+      3300          69   6.1499191      2.2106063      1.487616       0.49067642   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          79   5.285068       1.8038634      1.2153135      0.54139582   
+      3500          79   5.2666274      1.7830175      1.1995458      0.55459427   
+      3600          79   5.3876859      1.9198663      1.293578       0.49850619   
+      3700          79   5.1383103      1.6379635      1.1293018      0.47695008   
+      3800          79   5.2440711      1.7575191      1.2055687      0.48710695   
+      3900          79   5.2012402      1.7091016      1.1822768      0.47985425   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4000          86   4.7629755      1.5405815      1.0729745      0.50168305   
+      4100          86   4.8116324      1.5950004      1.1107717      0.483217     
+      4200          86   4.698988       1.4690165      1.0162879      0.67403453   
+      4300          86   4.8348111      1.6209239      1.105696       0.48548859   
+      4400          86   4.9124435      1.7077496      1.1582583      0.51373609   
+      4500          86   4.9206356      1.7169118      1.1667418      0.48432388   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          92   4.831251       1.8521355      1.2581902      0.50814475   
+      4700          92   4.9541337      1.9885054      1.3496439      0.5518164    
+      4800          92   5.0387054      2.0823594      1.425245       0.56425459   
+      4900          92   4.8856072      1.9124576      1.3459733      0.5410045    
+      5000          92   4.8601367      1.8841916      1.3063393      0.57580057   
+      5100         104   4.3795169      1.7374629      1.2066873      0.58493857   
+      5200         104   4.380644       1.7386979      1.2509659      0.50835208   
+      5300         104   4.4901754      1.8587164      1.3020409      0.55360586   
+      5400         104   4.4454236      1.8096798      1.2487279      0.90957267   
+      5500         104   4.3141875      1.6658786      1.138758       0.53403954   
+      5600         104   4.2764169      1.6244916      1.1094266      0.65043467   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      5700         108   4.2683501      1.7239258      1.1727672      0.67160605   
+      5800         108   4.4204385      1.8899816      1.2769697      0.67686418   
+      5900         108   4.4764852      1.9511754      1.3107129      0.64264496   
+      6000         108   4.5530001      2.0347172      1.3710873      0.87709467   
+      6100         108   4.5436906      2.0245527      1.3721167      0.66133934   
+      6200         108   4.4256297      1.8956495      1.28211        0.61859323   
+      6300         109   4.4477168      1.9452998      1.3215253      0.65196709   
+      6400         109   4.5512937      2.0582928      1.4082655      0.63769354   
+      6500         109   4.1366008      1.6059006      1.0940711      0.73216085   
+      6600         109   4.0674318      1.5304435      1.0397138      0.54093108   
+      6700         109   4.1348468      1.6039871      1.0852573      0.56630918   
+      6800         109   4.1430428      1.6129282      1.0943172      0.69178634   
+      6900         109   4.0543146      1.5161338      1.0197644      0.63108285   
+      7000         109   4.0838002      1.5482999      1.0407391      0.5748685    
+      7100         109   4.1521096      1.6228193      1.0928425      0.56509731   
+      7200         109   4.2124442      1.6886388      1.1348358      0.57024309   
+      7300         109   4.3441285      1.8322944      1.2309535      0.55057491   
+      7400         109   4.4552392      1.9535062      1.3185298      0.57664423   
+      7500         109   4.6386117      2.1535488      1.4543864      0.59727363   
+      7600         109   4.8049773      2.3350386      1.5852377      0.61684981   
+      7700         109   5.0774428      2.6322737      1.7974351      0.6717935    
+      7800         109   5.137687       2.6979946      1.8459588      0.71615719   
+      7900         109   5.2761666      2.8490633      1.9573222      0.66913482   
+      8000         108   5.2408428      2.7857291      1.9179915      0.70758627   
+      8100         107   4.9219903      2.4119819      1.6414735      0.67384853   
+      8200         105   4.88649        2.3202761      1.5738581      0.58235547   
+      8300         105   5.1910655      2.6537061      1.7940904      0.64215432   
+      8400         103   5.2358927      2.6483047      1.8075842      0.65624924   
+      8500         101   5.1028866      2.445274       1.6730309      0.91849673   
+      8600         100   4.8817968      2.1725461      1.4906124      0.59208611   
+      8700          97   4.7804409      1.9672828      1.3520376      0.5666713    
+      8800          97   4.6872197      1.8644179      1.2830232      0.62172034   
+      8900          97   4.5268118      1.6874162      1.159267       0.55290924   
+      9000          95   4.5196336      1.6126686      1.1077501      0.58828852   
+      9100          95   4.4232371      1.5060654      1.0318533      0.49357574   
+      9200          94   4.5096768      1.5670383      1.0651294      0.52806219   
+      9300          94   4.5673055      1.6308414      1.1051788      0.60308191   
+      9400          94   4.7375978      1.8193794      1.235354       0.52984284   
+      9500          94   4.8870798      1.9848774      1.3398669      0.54526912   
+      9600          94   5.1128471      2.2348339      1.504691       0.58238093   
+      9700          94   5.0933367      2.2132331      1.499447       0.64046557   
+      9800          94   4.9158399      2.0167189      1.377884       0.61716162   
+      9900          93   4.905138       1.9699273      1.3392297      0.56563086   
+     10000          93   4.7728825      1.8233309      1.2460043      0.62103726   
+Loop time of 0.670914 on 4 procs for 10000 steps with 93 atoms
+
+Performance: 6438981.671 tau/day, 14905.050 timesteps/s, 1.386 Matom-step/s
+92.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0060352  | 0.012089   | 0.021126   |   5.2 |  1.80
+Neigh   | 0.0047076  | 0.0094254  | 0.015055   |   3.9 |  1.40
+Comm    | 0.063432   | 0.075753   | 0.083566   |   3.0 | 11.29
+Output  | 0.27651    | 0.39883    | 0.54452    |  16.3 | 59.45
+Modify  | 0.015515   | 0.016152   | 0.01725    |   0.5 |  2.41
+Other   |            | 0.1587     |            |       | 23.65
+
+Nlocal:          23.25 ave          49 max           7 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:          23.25 ave          32 max          14 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 1467
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.line.gran.global.g++.1

@@ -0,0 +1,219 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+Created orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+molecule        lines surf.line
+Read molecule template lines:
+LAMMPS molecule file for line box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  9 lines with 11 points
+
+fix             20 all surface/global lines hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global lines hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+# rotate the box
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 -1 0
+#fix             4 all viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 fix 20 type 0.5 0.0
+dump_modify	2 pad 5
+
+run	        10000
+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 = 47 47 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.757 | 5.757 | 5.757 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100           7   1.0483784      1.0483784      0.66213376     0.0069891897 
+       200           7   1.6167923      1.6167923      1.0211319      0.010778615  
+       300           7   2.3379224      2.3379224      1.4765825      0.015586149  
+       400           7   3.2117688      3.2117688      2.0284855      0.021411792  
+       500           7   4.2383315      4.2383315      2.676841       0.028255543  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          18   2.1129055      2.1129055      1.3869354      0.039910437  
+       700          18   2.6043792      2.6043792      1.7214254      0.063754392  
+       800          18   2.8677827      2.8677827      1.9147069      0.054169228  
+       900          18   3.1228891      3.1228891      2.1263001      0.059201028  
+      1000          18   2.9398046      2.9398046      2.0739419      0.086537278  
+      1100          18   2.5261889      2.5261889      1.8187978      0.12454808   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          26   1.8985781      1.8985781      1.2816098      0.058565477  
+      1300          26   1.7554241      1.7554241      1.2048448      0.050988843  
+      1400          26   1.7859543      1.7859543      1.2306073      0.054608317  
+      1500          26   2.013552       2.013552       1.3984072      0.058664544  
+      1600          26   2.2374064      2.2374064      1.548047       0.063825039  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          36   2.1026641      2.1026641      1.4164548      0.090879302  
+      1800          36   2.221153       2.221153       1.4818344      0.14617071   
+      1900          36   2.2344917      2.2344917      1.4850053      0.14491866   
+      2000          36   2.162057       2.162057       1.4483877      0.10962255   
+      2100          36   2.0490205      2.0490205      1.371803       0.10269632   
+      2200          36   2.0245485      2.0245485      1.3453701      0.089476431  
+      2300          48   1.6035919      1.6035919      1.0816887      0.1462717    
+      2400          48   1.5727178      1.5727178      1.0558651      0.13036507   
+      2500          48   1.6133884      1.6133884      1.0809644      0.11153652   
+      2600          48   1.7297828      1.7297828      1.1672461      0.11279238   
+      2700          48   1.6146016      1.6146016      1.1097429      0.11088332   
+      2800          48   1.6951748      1.6951748      1.166744       0.096514604  
+      2900          60   1.8416564      1.8416564      1.2540668      0.14915168   
+      3000          60   2.1003861      2.1003861      1.4392908      0.14801032   
+      3100          60   2.2828232      2.2828232      1.556736       0.15616608   
+      3200          60   2.1222828      2.1222828      1.4349318      0.20907466   
+      3300          60   1.9967087      1.9967087      1.3527156      0.33475251   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          67   1.7019207      1.7019207      1.1573194      0.21087521   
+      3500          67   1.7833499      1.7833499      1.2070513      0.1780625    
+      3600          67   1.7577191      1.7577191      1.1996856      0.28041006   
+      3700          67   1.7607556      1.7607556      1.2011069      0.15554549   
+      3800          67   1.8033884      1.8033884      1.2321274      0.17400045   
+      3900          67   1.6362949      1.6362949      1.1260761      0.17584879   
+      4000          79   1.6044993      1.6044993      1.095751       0.15524341   
+      4100          79   1.6440518      1.6440518      1.1367568      0.18985067   
+      4200          79   1.4972418      1.4972418      1.0384732      0.18741202   
+      4300          79   1.6170109      1.6170109      1.1016272      0.15651659   
+      4400          79   1.8928159      1.8928159      1.2782002      0.18144602   
+      4500          79   1.9936679      1.9936679      1.3475771      0.20164039   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          90   1.8140729      1.8140729      1.24197        0.31384373   
+      4700          90   2.0254763      2.0254763      1.384261       0.23627572   
+      4800          90   1.9114718      1.9114718      1.2955738      0.24021925   
+      4900          90   1.9776905      1.9776905      1.3575896      0.31285969   
+      5000          90   1.970076       1.970076       1.3376466      0.25423539   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      5100          97   1.7820291      1.7820291      1.2227938      0.36718321   
+      5200          97   1.7597485      1.7597485      1.2119527      0.27764658   
+      5300          97   1.8501223      1.8501223      1.2722665      0.2360191    
+      5400          97   1.6078405      1.6078405      1.0908201      0.32910986   
+      5500          97   1.6928997      1.6928997      1.1522543      0.25113312   
+      5600          97   1.7992766      1.7992766      1.2196839      0.34494996   
+      5700         100   1.7649055      1.7649055      1.1911619      0.36582075   
+      5800         100   1.9223565      1.9223565      1.2879921      0.28447504   
+      5900         100   1.9444004      1.9444004      1.3064959      0.3754893    
+      6000         100   1.9270809      1.9270809      1.3050329      0.37763816   
+      6100         100   2.0085556      2.0085556      1.3508579      0.28069022   
+      6200         100   1.8722285      1.8722285      1.270563       0.39005335   
+      6300         100   1.8274778      1.8274778      1.2443066      0.28375094   
+      6400         100   1.8520157      1.8520157      1.2633763      0.27216291   
+      6500         100   1.787681       1.787681       1.2218869      0.25732165   
+      6600         100   1.7226268      1.7226268      1.1638035      0.27501256   
+      6700         100   1.5680255      1.5680255      1.0574623      0.20532645   
+      6800         100   1.5457817      1.5457817      1.0457377      0.20982707   
+      6900         100   1.5847886      1.5847886      1.0652338      0.26944126   
+      7000         100   1.6088044      1.6088044      1.0792231      0.2316201    
+      7100         100   1.7081624      1.7081624      1.1436866      0.33210417   
+      7200         100   1.8245918      1.8245918      1.2219392      0.2337092    
+      7300         100   1.9177685      1.9177685      1.2897955      0.30095141   
+      7400         100   2.0540287      2.0540287      1.3801642      0.25456251   
+      7500         100   2.2039085      2.2039085      1.4820949      0.28834324   
+      7600         100   2.259514       2.259514       1.5282738      0.28491233   
+      7700         100   2.5155549      2.5155549      1.7074936      0.3152297    
+      7800         100   2.6870643      2.6870643      1.8312269      0.35440174   
+      7900         100   2.4727714      2.4727714      1.703333       0.36829004   
+      8000         100   2.6276081      2.6276081      1.7884458      0.32525675   
+      8100          99   2.5924836      2.5924836      1.7709533      0.37086875   
+      8200          99   2.7395551      2.7395551      1.8614194      0.38872251   
+      8300          96   2.6217174      2.6217174      1.7750969      0.29386994   
+      8400          94   2.3453973      2.3453973      1.5915715      0.25246126   
+      8500          92   2.2746092      2.2746092      1.5522863      0.31979019   
+      8600          91   2.0971668      2.0971668      1.4441167      0.23164239   
+      8700          90   1.9520436      1.9520436      1.3407037      0.2267317    
+      8800          88   1.6031029      1.6031029      1.1075422      0.22893706   
+      8900          88   1.3714136      1.3714136      0.95329267     0.1449532    
+      9000          88   1.3999833      1.3999833      0.96786566     0.17754279   
+      9100          88   1.5308757      1.5308757      1.0447361      0.1886558    
+      9200          88   1.5573847      1.5573847      1.0593305      0.16600982   
+      9300          86   1.5666806      1.5666806      1.065567       0.18426275   
+      9400          86   1.7748404      1.7748404      1.1960622      0.19566408   
+      9500          86   1.8680619      1.8680619      1.2596475      0.2541481    
+      9600          86   2.0507836      2.0507836      1.3819586      0.27903247   
+      9700          86   2.1304474      2.1304474      1.4467793      0.36641932   
+      9800          85   2.0665993      2.0665993      1.4185404      0.21957531   
+      9900          85   2.2152558      2.2152558      1.5009933      0.2464896    
+     10000          85   2.2236372      2.2236372      1.5032593      0.2873953    
+Loop time of 0.330199 on 1 procs for 10000 steps with 85 atoms
+
+Performance: 13083014.205 tau/day, 30284.755 timesteps/s, 2.574 Matom-step/s
+91.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.014535   | 0.014535   | 0.014535   |   0.0 |  4.40
+Neigh   | 0.0077843  | 0.0077843  | 0.0077843  |   0.0 |  2.36
+Comm    | 0.0007947  | 0.0007947  | 0.0007947  |   0.0 |  0.24
+Output  | 0.27492    | 0.27492    | 0.27492    |   0.0 | 83.26
+Modify  | 0.029972   | 0.029972   | 0.029972   |   0.0 |  9.08
+Other   |            | 0.002194   |            |       |  0.66
+
+Nlocal:             85 ave          85 max          85 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:            125 ave         125 max         125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 125
+Ave neighs/atom = 1.4705882
+Neighbor list builds = 1465
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.line.gran.global.g++.4

@@ -0,0 +1,220 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+Created orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  2 by 2 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+molecule        lines surf.line
+Read molecule template lines:
+LAMMPS molecule file for line box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  9 lines with 11 points
+
+fix             20 all surface/global lines hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global lines hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+# rotate the box
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 -1 0
+#fix             4 all viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 fix 20 type 0.5 0.0
+dump_modify	2 pad 5
+
+run	        10000
+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 = 47 47 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.765 | 5.765 | 5.765 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100           7   1.0483784      1.0483784      0.66213376     0.0069891897 
+       200           7   1.6167923      1.6167923      1.0211319      0.010778615  
+       300           7   2.3379224      2.3379224      1.4765825      0.015586149  
+       400           7   3.2117688      3.2117688      2.0284855      0.021411792  
+       500           7   4.2383315      4.2383315      2.676841       0.028255543  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          18   2.1129055      2.1129055      1.3869354      0.039910437  
+       700          18   2.6043792      2.6043792      1.7214254      0.063754392  
+       800          18   2.8677827      2.8677827      1.9147069      0.054169228  
+       900          18   3.1228891      3.1228891      2.1263001      0.059201028  
+      1000          18   2.9398046      2.9398046      2.0739419      0.086537278  
+      1100          18   2.5261889      2.5261889      1.8187978      0.12454808   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          26   1.8985781      1.8985781      1.2816098      0.058565477  
+      1300          26   1.7554241      1.7554241      1.2048448      0.050988843  
+      1400          26   1.7859543      1.7859543      1.2306073      0.054608317  
+      1500          26   2.013552       2.013552       1.3984072      0.058664544  
+      1600          26   2.2374064      2.2374064      1.548047       0.063825039  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          36   2.1026641      2.1026641      1.4164548      0.090879302  
+      1800          36   2.221153       2.221153       1.4818344      0.14617071   
+      1900          36   2.2344917      2.2344917      1.4850053      0.14491866   
+      2000          36   2.162057       2.162057       1.4483877      0.10962255   
+      2100          36   2.0490205      2.0490205      1.371803       0.10269632   
+      2200          36   2.0245485      2.0245485      1.3453701      0.089476431  
+      2300          48   1.6035919      1.6035919      1.0816887      0.1462717    
+      2400          48   1.5727178      1.5727178      1.0558651      0.13036507   
+      2500          48   1.6133884      1.6133884      1.0809644      0.11153652   
+      2600          48   1.7297828      1.7297828      1.1672461      0.11279238   
+      2700          48   1.6146016      1.6146016      1.1097429      0.11088332   
+      2800          48   1.6951748      1.6951748      1.166744       0.096514605  
+      2900          60   1.8416564      1.8416564      1.2540668      0.14915169   
+      3000          60   2.100386       2.100386       1.4392907      0.1480102    
+      3100          60   2.2828225      2.2828225      1.5567356      0.15616606   
+      3200          60   2.1222644      2.1222644      1.4349199      0.20907562   
+      3300          60   1.9966845      1.9966845      1.3527006      0.33472885   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          67   1.7019235      1.7019235      1.1573204      0.2108847    
+      3500          67   1.7833138      1.7833138      1.2070182      0.17801747   
+      3600          67   1.7569994      1.7569994      1.1991783      0.28231225   
+      3700          67   1.7571831      1.7571831      1.1993044      0.14987615   
+      3800          67   1.8019878      1.8019878      1.2311475      0.16225609   
+      3900          67   1.6358579      1.6358579      1.126536       0.17569967   
+      4000          79   1.6034602      1.6034602      1.0941546      0.16756481   
+      4100          79   1.6366467      1.6366467      1.1340817      0.16064361   
+      4200          79   1.4730958      1.4730958      1.0141142      0.16287858   
+      4300          79   1.5906033      1.5906033      1.0817142      0.1625915    
+      4400          79   1.8936552      1.8936552      1.2861135      0.17579343   
+      4500          79   2.0727626      2.0727626      1.402595       0.19190637   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          90   1.8869572      1.8869572      1.2792715      0.34462947   
+      4700          90   2.0639296      2.0639296      1.3938374      0.34201338   
+      4800          90   1.9341543      1.9341543      1.3359686      0.21954974   
+      4900          90   1.9328058      1.9328058      1.318194       0.22883244   
+      5000          90   1.8713075      1.8713075      1.2779328      0.4301643    
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      5100          97   1.8889201      1.8889201      1.2901598      0.4621263    
+      5200          97   1.8182665      1.8182665      1.2499619      0.35152238   
+      5300          97   1.8955183      1.8955183      1.3251783      0.26911868   
+      5400          97   1.698589       1.698589       1.1591879      0.30370185   
+      5500          97   1.7599832      1.7599832      1.1979596      0.32792377   
+      5600          97   1.7770974      1.7770974      1.211641       0.31929074   
+      5700         100   1.7803057      1.7803057      1.2040432      0.35291347   
+      5800         100   1.926965       1.926965       1.3003468      0.27956044   
+      5900         100   2.0526934      2.0526934      1.3834338      0.31887573   
+      6000         100   2.1044137      2.1044137      1.4099441      0.29869407   
+      6100         100   2.0230041      2.0230041      1.3669222      0.28123514   
+      6200         100   2.0312769      2.0312769      1.3817115      0.30601616   
+      6300         100   2.0551063      2.0551063      1.393468       0.29181867   
+      6400         100   1.8164349      1.8164349      1.2965294      0.25696247   
+      6500         100   1.6499854      1.6499854      1.1522945      0.26606593   
+      6600         100   1.5859571      1.5859571      1.079181       0.23976532   
+      6700         100   1.5818463      1.5818463      1.0729409      0.22487518   
+      6800         100   1.5370121      1.5370121      1.037886       0.20497101   
+      6900         100   1.5636721      1.5636721      1.0493528      0.24001323   
+      7000         100   1.625322       1.625322       1.0927408      0.21871244   
+      7100         100   1.6516426      1.6516426      1.1089036      0.24426204   
+      7200         100   1.8158528      1.8158528      1.2225264      0.24120862   
+      7300         100   2.0003553      2.0003553      1.3472959      0.2565553    
+      7400         100   2.2073583      2.2073583      1.4799781      0.27501492   
+      7500         100   2.4331081      2.4331081      1.6366984      0.2964906    
+      7600         100   2.4714321      2.4714321      1.6795351      0.41204677   
+      7700         100   2.722459       2.722459       1.859155       0.34849871   
+      7800         100   2.971029       2.971029       2.0560731      0.3575871    
+      7900         100   2.5988892      2.5988892      1.8002454      0.39841917   
+      8000         100   2.7119251      2.7119251      1.8535416      0.3339011    
+      8100          98   2.6035719      2.6035719      1.787137       0.30161331   
+      8200          95   2.4913394      2.4913394      1.709658       0.29609108   
+      8300          94   2.5446704      2.5446704      1.7329605      0.38074      
+      8400          93   2.7108353      2.7108353      1.8449224      0.29338784   
+      8500          89   2.4397796      2.4397796      1.66773        0.30167351   
+      8600          89   2.3096796      2.3096796      1.5987688      0.34829767   
+      8700          86   1.9343795      1.9343795      1.3483427      0.26186082   
+      8800          85   1.7530569      1.7530569      1.2210598      0.20667183   
+      8900          85   1.7846979      1.7846979      1.228582       0.2354851    
+      9000          85   1.5864774      1.5864774      1.0853295      0.23148728   
+      9100          83   1.4761406      1.4761406      1.0104611      0.14783417   
+      9200          82   1.4764644      1.4764644      1.0104747      0.16107786   
+      9300          82   1.5656948      1.5656948      1.0633005      0.25375701   
+      9400          82   1.6651149      1.6651149      1.1242623      0.17702309   
+      9500          82   1.8295914      1.8295914      1.2294728      0.20502222   
+      9600          82   1.9868742      1.9868742      1.3460986      0.20899366   
+      9700          81   1.9123665      1.9123665      1.2957378      0.18989899   
+      9800          81   1.9032788      1.9032788      1.2877863      0.32372042   
+      9900          81   1.9686313      1.9686313      1.3389864      0.24692959   
+     10000          81   2.0160999      2.0160999      1.3612427      0.22858996   
+Loop time of 0.59471 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 7264049.619 tau/day, 16814.930 timesteps/s, 1.362 Matom-step/s
+94.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00098431 | 0.0046234  | 0.0099857  |   5.0 |  0.78
+Neigh   | 0.0012879  | 0.0026652  | 0.0043266  |   2.2 |  0.45
+Comm    | 0.029312   | 0.033471   | 0.038201   |   1.8 |  5.63
+Output  | 0.31437    | 0.39643    | 0.52119    |  13.5 | 66.66
+Modify  | 0.012135   | 0.017152   | 0.023684   |   3.4 |  2.88
+Other   |            | 0.1404     |            |       | 23.60
+
+Nlocal:          20.25 ave          44 max           5 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:            3.5 ave           7 max           0 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:          26.75 ave          68 max           1 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 107
+Ave neighs/atom = 1.3209877
+Neighbor list builds = 1469
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.line.gran.surf.g++.1

@@ -0,0 +1,233 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+Created orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  1 by 1 by 1 MPI processor grid
+
+molecule        lines surf.line
+Read molecule template lines:
+LAMMPS molecule file for line box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  9 lines
+fix             20 all surface/local lines
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           line type 2
+9 atoms in group line
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run	       10000
+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 = 6.0201533
+  ghost atom cutoff = 6.0201533
+  binsize = 3.0100766, bins = 10 10 1
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair line/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.08 | 12.08 | 12.08 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           9   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          16   19.603933      1.0483784      0.66213376     0.32673222   
+       200          16   19.831299      1.6167923      1.0211319      0.33052165   
+       300          16   20.119751      2.3379224      1.4765825      0.33532918   
+       400          16   20.469289      3.2117688      2.0284855      0.34115482   
+       500          16   20.879914      4.2383315      2.676841       0.34799857   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          27   12.449543      2.1129055      1.3869354      0.35243867   
+       700          27   12.770891      2.6043792      1.7214254      0.38349742   
+       800          27   12.943117      2.8677827      1.9147069      0.37516936   
+       900          27   13.109917      3.1228891      2.1263001      0.38019376   
+      1000          27   12.990208      2.9398046      2.0739419      0.42599315   
+      1100          27   12.719767      2.5261889      1.8187978      0.45457071   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          35   9.8597994      1.8985781      1.2816098      0.38022839   
+      1300          35   9.7545391      1.7554241      1.2048448      0.37276257   
+      1400          35   9.7769878      1.7859543      1.2306073      0.37760148   
+      1500          35   9.9443391      2.013552       1.3984072      0.38116488   
+      1600          35   10.108938      2.2374064      1.548047       0.38622523   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          45   8.2127721      2.1026641      1.4164548      0.41493848   
+      1800          45   8.3070246      2.221153       1.4818344      0.48996397   
+      1900          45   8.3176349      2.2344917      1.4850053      0.47813979   
+      2000          45   8.2600165      2.162057       1.4483877      0.43264535   
+      2100          45   8.170101       2.0490205      1.371803       0.4264254    
+      2200          45   8.1506346      2.0245485      1.3453701      0.41836913   
+      2300          57   6.484599       1.6035919      1.0816888      0.47342867   
+      2400          57   6.4586868      1.5727177      1.0558651      0.46664108   
+      2500          57   6.4928211      1.6133884      1.0809644      0.44246689   
+      2600          57   6.5905095      1.7297831      1.1672463      0.44469826   
+      2700          57   6.4938379      1.6145999      1.1097418      0.44349717   
+      2800          57   6.561462       1.6951733      1.1667434      0.42184931   
+      2900          69   5.8294334      1.8412329      1.2537935      0.47920761   
+      3000          69   6.0530502      2.0989608      1.4383292      0.47115384   
+      3100          69   6.2128755      2.2831662      1.5569471      0.48035619   
+      3200          69   6.0796177      2.1295809      1.4395228      0.59719942   
+      3300          69   5.9598587      1.9915536      1.3476382      0.70904872   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          76   5.3278321      1.6942225      1.1512533      0.55750722   
+      3500          76   5.3580089      1.7285142      1.1733033      0.48015375   
+      3600          76   5.3912511      1.7662894      1.2244098      0.53667674   
+      3700          76   5.3915755      1.7666581      1.2023862      0.50933582   
+      3800          76   5.5024499      1.8926518      1.2816818      0.49183973   
+      3900          76   5.2931801      1.6548451      1.1449579      0.54259885   
+      4000          88   4.7587858      1.6185338      1.1148203      0.50111437   
+      4100          88   4.6686812      1.5180325      1.0739014      0.53207092   
+      4200          88   4.704383       1.5578537      1.0828675      0.48968011   
+      4300          88   4.8151499      1.6814015      1.1458567      0.54476462   
+      4400          88   4.9536407      1.835872       1.2370382      0.50443506   
+      4500          88   5.1049527      2.004643       1.3561346      0.63246898   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          97   4.6429295      1.815546       1.2258897      0.76318653   
+      4700          97   4.7557974      1.94009        1.3308417      0.58800825   
+      4800          97   4.7588482      1.9434563      1.3238059      0.54808039   
+      4900          97   4.7816962      1.9686679      1.3555958      0.57086836   
+      5000          97   4.7081833      1.8875502      1.2938704      0.53341015   
+      5100         109   4.2946936      1.7783655      1.2235441      0.74414659   
+      5200         109   4.4514423      1.9493641      1.3382034      0.5816121    
+      5300         109   4.3031748      1.7876177      1.2509563      0.64288295   
+      5400         109   4.1392053      1.6087418      1.1007772      0.56520057   
+      5500         109   4.1921177      1.6664644      1.1482381      0.64655034   
+      5600         109   4.1978214      1.6726867      1.1442267      0.62708256   
+      5700         109   4.2167733      1.6933615      1.149386       0.58370357   
+      5800         109   4.4043993      1.8980444      1.2841934      0.59795187   
+      5900         109   4.4714853      1.9712292      1.3223473      0.70540432   
+      6000         109   4.4233763      1.9187466      1.2856953      0.74824095   
+      6100         109   4.5032352      2.0058654      1.3516717      0.69570797   
+      6200         109   4.4767193      1.9769389      1.3333093      0.68696926   
+      6300         109   4.3959917      1.8888725      1.2907122      0.63303162   
+      6400         109   4.3835668      1.875318       1.3074197      0.63844057   
+      6500         109   4.2555571      1.7356711      1.2015655      0.66131926   
+      6600         109   4.0671476      1.5301335      1.038876       0.583031     
+      6700         109   4.0619437      1.5244565      1.0254465      0.57917715   
+      6800         109   4.0744984      1.5381525      1.0362496      0.57031315   
+      6900         109   4.0970582      1.5627632      1.0516772      0.56180234   
+      7000         109   4.1712104      1.6436565      1.104496       0.57061264   
+      7100         109   4.2194438      1.6962748      1.1401819      0.55033817   
+      7200         109   4.2854688      1.7683021      1.1878994      0.64255961   
+      7300         109   4.4439681      1.9412104      1.3032284      0.57856127   
+      7400         109   4.6570939      2.1737112      1.4593098      0.62381538   
+      7500         109   4.8364799      2.369405       1.5988389      0.63335535   
+      7600         109   4.9865193      2.5330844      1.7216312      0.63560865   
+      7700         109   5.0603314      2.6136067      1.7991217      0.67457582   
+      7800         109   5.2825153      2.8559892      1.9752674      0.69847738   
+      7900         109   4.9404332      2.4828087      1.6955058      0.86486934   
+      8000         109   4.9666953      2.5114582      1.7172461      0.68914422   
+      8100         108   4.9305596      2.4469505      1.6692969      0.65720524   
+      8200         107   5.0171731      2.5159961      1.7141712      0.64962298   
+      8300         106   5.1706019      2.6577549      1.7991671      0.6533149    
+      8400         104   5.1183939      2.5470834      1.7426175      0.71014805   
+      8500         104   5.0286833      2.4487835      1.6635557      0.70734083   
+      8600         102   4.8364284      2.1816363      1.4906665      0.72649249   
+      8700         101   4.7693385      2.0787376      1.419965       0.73442515   
+      8800         101   4.6195384      1.9141221      1.3207731      0.63177233   
+      8900          99   4.4786741      1.6982172      1.1718512      0.50697976   
+      9000          98   4.4490307      1.633946       1.1374461      0.57834948   
+      9100          98   4.3269215      1.4993484      1.0212072      0.61915381   
+      9200          98   4.4129354      1.5941592      1.0769509      0.51649969   
+      9300          97   4.3960432      1.5431198      1.0434136      0.51272277   
+      9400          96   4.47939        1.6020154      1.077862       0.53500446   
+      9500          96   4.6658982      1.8080419      1.2161966      0.5668484    
+      9600          96   4.7814753      1.9357142      1.3019606      0.56842177   
+      9700          96   4.8817258      2.0464561      1.3793406      0.5434597    
+      9800          96   4.8897807      2.055354       1.4031051      0.57800149   
+      9900          96   4.7789147      1.9328857      1.3227732      0.64989251   
+     10000          96   4.8776914      2.0419995      1.3827425      0.61157291   
+Loop time of 0.360523 on 1 procs for 10000 steps with 96 atoms
+
+Performance: 11982585.509 tau/day, 27737.466 timesteps/s, 2.663 Matom-step/s
+94.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.030975   | 0.030975   | 0.030975   |   0.0 |  8.59
+Neigh   | 0.028971   | 0.028971   | 0.028971   |   0.0 |  8.04
+Comm    | 0.0010264  | 0.0010264  | 0.0010264  |   0.0 |  0.28
+Output  | 0.28234    | 0.28234    | 0.28234    |   0.0 | 78.31
+Modify  | 0.014786   | 0.014786   | 0.014786   |   0.0 |  4.10
+Other   |            | 0.002423   |            |       |  0.67
+
+Nlocal:             96 ave          96 max          96 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 1470
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.line.gran.surf.g++.4

@@ -0,0 +1,234 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of line segments
+
+units		lj
+atom_style	line
+atom_modify     map array
+boundary        f f p
+dimension	2
+comm_modify     vel yes
+
+region		box block -15 15 -15 15 -0.5 0.5 units box
+create_box	2 box
+Created orthogonal box = (-15 -15 -0.5) to (15 15 0.5)
+  2 by 2 by 1 MPI processor grid
+
+molecule        lines surf.line
+Read molecule template lines:
+LAMMPS molecule file for line box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  9 lines
+fix             20 all surface/local lines
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 line/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 line/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           line type 2
+9 atoms in group line
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 90
+
+# rotate the box
+
+fix             1 line move rotate 0 0 0 0 0 1 25
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 -1 0
+#fix             4 sphere viscous 0.2
+
+region          slab block -3 3 -2 2 -0.5 0.5 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab
+Particle insertion: 12 every 566 steps, 100 by step 4529
+
+fix		10 all enforce2d
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.6 adiam 1.0 line type 0.5
+dump_modify	2 pad 5
+
+run	       10000
+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 = 6.0201533
+  ghost atom cutoff = 6.0201533
+  binsize = 3.0100766, bins = 10 10 1
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair line/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           9   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          16   19.603933      1.0483784      0.66213376     0.32673222   
+       200          16   19.831299      1.6167923      1.0211319      0.33052165   
+       300          16   20.119751      2.3379224      1.4765825      0.33532918   
+       400          16   20.469289      3.2117688      2.0284855      0.34115482   
+       500          16   20.879914      4.2383315      2.676841       0.34799857   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          27   12.449543      2.1129055      1.3869354      0.35243867   
+       700          27   12.770891      2.6043792      1.7214254      0.38349742   
+       800          27   12.943117      2.8677827      1.9147069      0.37516936   
+       900          27   13.109917      3.1228891      2.1263001      0.38019376   
+      1000          27   12.990208      2.9398046      2.0739419      0.42599315   
+      1100          27   12.719767      2.5261889      1.8187978      0.45457071   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          35   9.8597994      1.8985781      1.2816098      0.38022839   
+      1300          35   9.7545391      1.7554241      1.2048448      0.37276257   
+      1400          35   9.7769878      1.7859543      1.2306073      0.37760148   
+      1500          35   9.9443391      2.013552       1.3984072      0.38116488   
+      1600          35   10.108938      2.2374064      1.548047       0.38622523   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1700          45   8.2127721      2.1026641      1.4164548      0.41493848   
+      1800          45   8.3070246      2.221153       1.4818344      0.48996397   
+      1900          45   8.3176349      2.2344917      1.4850053      0.47813979   
+      2000          45   8.2600165      2.162057       1.4483877      0.43264535   
+      2100          45   8.170101       2.0490205      1.371803       0.4264254    
+      2200          45   8.1506346      2.0245485      1.3453701      0.41836913   
+      2300          57   6.484599       1.6035919      1.0816888      0.47342867   
+      2400          57   6.4586868      1.5727177      1.0558651      0.46664108   
+      2500          57   6.4928211      1.6133884      1.0809644      0.44246689   
+      2600          57   6.5905095      1.7297831      1.1672463      0.44469826   
+      2700          57   6.4938379      1.6145999      1.1097418      0.44349717   
+      2800          57   6.561462       1.6951733      1.1667434      0.42184931   
+      2900          69   5.8294333      1.8412328      1.2537935      0.47920762   
+      3000          69   6.0530502      2.0989608      1.4383292      0.4711539    
+      3100          69   6.2128757      2.2831664      1.5569472      0.48035613   
+      3200          69   6.0796163      2.1295793      1.4395217      0.59719777   
+      3300          69   5.9598651      1.991561       1.3476432      0.70904083   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      3400          76   5.3280254      1.6944421      1.1509347      0.55607697   
+      3500          76   5.3586022      1.7291884      1.1738073      0.48154419   
+      3600          76   5.3960594      1.7717535      1.2255034      0.50328012   
+      3700          76   5.392702       1.7679382      1.2006691      0.55300787   
+      3800          76   5.487271       1.875403       1.2701996      0.49070261   
+      3900          76   5.2631187      1.6206845      1.124056       0.53950667   
+      4000          88   4.7552309      1.6145687      1.1102653      0.50396334   
+      4100          88   4.7298672      1.5862785      1.1187972      0.48548654   
+      4200          88   4.7568479      1.6163722      1.1239114      0.49520917   
+      4300          88   4.899206       1.7751563      1.1996402      0.50485077   
+      4400          88   5.0855627      1.9830157      1.3306174      0.50684884   
+      4500          88   5.0860568      1.9835668      1.340137       0.51799838   
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      4600          97   4.7446937      1.9278375      1.3060898      0.55304468   
+      4700          97   4.8400782      2.0330894      1.3706834      0.59426453   
+      4800          97   4.6948697      1.8728594      1.2880301      0.65277707   
+      4900          97   4.6757748      1.8517891      1.2744619      0.55960057   
+      5000          97   4.6818196      1.8584593      1.2833187      0.56672558   
+      5100         109   4.2656545      1.7466864      1.2022774      0.72060325   
+      5200         109   4.4089285      1.9029854      1.303466       0.57487441   
+      5300         109   4.266038       1.7471048      1.2161309      0.76509931   
+      5400         109   4.0820492      1.5463898      1.0585873      0.59400707   
+      5500         109   4.2225625      1.699677       1.1633136      0.564166     
+      5600         109   4.2048922      1.6804004      1.1606267      0.55761391   
+      5700         109   4.25302        1.7329034      1.1803705      0.75579106   
+      5800         109   4.4166147      1.9113703      1.2934093      0.57750174   
+      5900         109   4.4963066      1.9983069      1.3522373      0.67654161   
+      6000         109   4.4487785      1.946458       1.3129991      0.65356753   
+      6100         109   4.3667261      1.8569464      1.2612208      0.63848496   
+      6200         109   4.4547267      1.9529471      1.3265293      0.63719023   
+      6300         109   4.3364884      1.8239598      1.2342374      0.65725781   
+      6400         109   4.3720247      1.8627267      1.2799281      0.59527799   
+      6500         109   4.2700467      1.7514779      1.2071184      0.79488752   
+      6600         109   4.1796078      1.6528174      1.1268666      0.54811483   
+      6700         109   4.1026903      1.5689073      1.0529781      0.55134253   
+      6800         109   4.0874552      1.5522872      1.0382647      0.55769258   
+      6900         109   4.0479731      1.5092158      1.0099323      0.53959573   
+      7000         109   4.0787277      1.5427663      1.0326475      0.55627473   
+      7100         109   4.1441         1.6140816      1.0811479      0.54441352   
+      7200         109   4.2104421      1.6864547      1.1296727      0.54213924   
+      7300         109   4.3919246      1.8844357      1.2652852      0.56502223   
+      7400         109   4.6135985      2.1262617      1.4292047      0.58413382   
+      7500         109   4.7432973      2.2677513      1.5329818      0.60724149   
+      7600         109   4.9384456      2.4806404      1.6880915      0.62523312   
+      7700         109   5.090558       2.6465812      1.8111403      0.6585716    
+      7800         109   5.3259416      2.9033632      2.0035146      0.6785935    
+      7900         109   5.2072113      2.7738393      1.895143       0.76755979   
+      8000         109   5.083771       2.6391772      1.8002856      0.66934075   
+      8100         108   4.937056       2.4540435      1.6848433      0.68706675   
+      8200         107   5.080298       2.584978       1.7670522      0.65360458   
+      8300         104   5.043418       2.464929       1.6753853      0.65112973   
+      8400         104   4.9112894      2.3201497      1.6035174      0.63202536   
+      8500         103   4.9725325      2.3594579      1.6178748      0.65226513   
+      8600         102   4.9240568      2.2778371      1.5557893      0.64939044   
+      8700         101   4.9182616      2.2423894      1.5252109      0.59242907   
+      8800          98   4.7809771      1.9998415      1.3609365      0.62824865   
+      8900          97   4.6171003      1.7870448      1.2279757      0.59541262   
+      9000          97   4.578037       1.7439405      1.2014952      0.53042665   
+      9100          96   4.3863917      1.4992847      1.0287029      0.53128022   
+      9200          95   4.4878465      1.5775158      1.0718141      0.50926528   
+      9300          95   4.4698544      1.5576187      1.0520012      0.55570417   
+      9400          94   4.5745795      1.6388948      1.1062354      0.52958404   
+      9500          94   4.682009       1.7578347      1.1869533      0.58337186   
+      9600          94   4.8288332      1.92039        1.2962606      0.54697385   
+      9700          94   4.9380546      2.0413137      1.3804181      0.56679619   
+      9800          94   4.9163917      2.0173297      1.3698459      0.58780334   
+      9900          94   4.9246764      2.0265021      1.3927278      0.65819328   
+     10000          94   4.7358922      1.817491       1.2533343      0.65922393   
+Loop time of 0.626598 on 4 procs for 10000 steps with 94 atoms
+
+Performance: 6894371.511 tau/day, 15959.193 timesteps/s, 1.500 Matom-step/s
+92.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0041891  | 0.011756   | 0.021395   |   6.0 |  1.88
+Neigh   | 0.0039448  | 0.0094415  | 0.015903   |   4.5 |  1.51
+Comm    | 0.063898   | 0.077286   | 0.086409   |   3.3 | 12.33
+Output  | 0.27418    | 0.36951    | 0.498      |  14.4 | 58.97
+Modify  | 0.015224   | 0.016492   | 0.018408   |   0.9 |  2.63
+Other   |            | 0.1421     |            |       | 22.68
+
+Nlocal:           23.5 ave          45 max           5 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:          24.75 ave          32 max          18 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 1474
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.data.g++.1

@@ -0,0 +1,357 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tri
+Reading data file ...
+  orthogonal box = (-7 -7 0) to (7 7 9)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4 atoms
+  4 triangles
+  read_data CPU = 0.001 seconds
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.33 | 13.33 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95075919     1.0392019      0.51601709     0.025332019  
+       600          48   0.84031896     0.91848817     0.4623667      0.022636752  
+       700          48   0.85874279     0.93862584     0.4826348      0.046371063  
+       800          48   0.73132774     0.79935822     0.43136382     0.022138279  
+       900          72   0.65995369     0.69935391     0.36547311     0.050914097  
+      1000          72   0.62313984     0.66034222     0.35115498     0.033703652  
+      1100          72   0.61206069     0.64860162     0.3482546      0.026726748  
+      1200          72   0.55722289     0.59048993     0.31886384     0.043718461  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.46095761     0.48215107     0.26148102     0.03655992   
+      1400          92   0.47463128     0.49645341     0.26932173     0.026649699  
+      1500          92   0.43876093     0.45893385     0.25112926     0.039053185  
+      1600          92   0.39781564     0.41610602     0.2336458      0.038915755  
+      1700         104   0.3314644      0.3448569      0.19379636     0.056687783  
+      1800         104   0.28818581     0.29982968     0.17211551     0.024813484  
+      1900         104   0.25183364     0.26200874     0.15328845     0.02192128   
+      2000         104   0.23713983     0.24672124     0.14327078     0.042148673  
+      2100         104   0.23506188     0.24455933     0.14029326     0.017721951  
+      2200         104   0.15864009     0.16504979     0.10412746     0.029964397  
+      2300         104   0.10670987     0.11102138     0.07871108     0.0071805097 
+      2400         104   0.076639282    0.079735819    0.060947043    0.015389321  
+      2500         103   0.055400086    0.057661314    0.044473443    0.015445498  
+      2600         103   0.035893374    0.03735841     0.028760404    0.01067378   
+      2700         102   0.03158966     0.032892327    0.023822829    0.0082275369 
+      2800         102   0.024365874    0.025370652    0.019216631    0.011973307  
+      2900         101   0.014440858    0.01504256     0.012197533    0.0072741624 
+      3000         101   0.013021269    0.013563822    0.011242148    0.010498718  
+      3100         101   0.010273872    0.010701951    0.0091143287   0.0072871705 
+      3200         101   0.0070740359   0.0073687874   0.0067970148   0.0064989269 
+      3300         101   0.0073212732   0.0076263262   0.0065171125   0.0098946739 
+      3400         101   0.0047267512   0.0049236991   0.0044264772   0.007575603  
+      3500         101   0.003264981    0.0034010219   0.0032263675   0.0064756429 
+      3600         101   0.0019366725   0.0020173672   0.0020455688   0.0067365178 
+      3700         101   0.0018126432   0.00188817     0.0019196352   0.0063300027 
+      3800         101   0.0019330301   0.002013573    0.0019421727   0.0066930211 
+      3900         101   0.0017022743   0.0017732024   0.0017692091   0.0063161884 
+      4000         101   0.0011235173   0.0011703305   0.0011857636   0.0062516843 
+      4100         101   0.0010738339   0.0011185769   0.0011489616   0.0061908407 
+      4200         101   0.0010663665   0.0011107985   0.0011562642   0.0061205723 
+      4300         101   0.0010325958   0.0010756206   0.001137752    0.0063715073 
+      4400         101   0.00088714248  0.00092410675  0.0010581337   0.0071315304 
+      4500         101   0.00072957163  0.00075997045  0.00089148584  0.0061822402 
+      4600         101   0.00072916208  0.00075954383  0.00093229962  0.0073336189 
+      4700         101   0.00049478944  0.00051540567  0.00062291356  0.0066293137 
+      4800         101   0.00049162494  0.00051210931  0.00063696192  0.0062116978 
+      4900         101   0.00041908773  0.00043654972  0.00059061447  0.0064909785 
+      5000         101   0.00040336839  0.0004201754   0.00059603372  0.0062594394 
+Loop time of 0.331047 on 1 procs for 5000 steps with 101 atoms
+
+Performance: 6524755.135 tau/day, 15103.600 timesteps/s, 1.525 Matom-step/s
+68.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.02908    | 0.02908    | 0.02908    |   0.0 |  8.78
+Neigh   | 0.0094722  | 0.0094722  | 0.0094722  |   0.0 |  2.86
+Comm    | 0.00045139 | 0.00045139 | 0.00045139 |   0.0 |  0.14
+Output  | 0.27825    | 0.27825    | 0.27825    |   0.0 | 84.05
+Modify  | 0.012533   | 0.012533   | 0.012533   |   0.0 |  3.79
+Other   |            | 0.001257   |            |       |  0.38
+
+Nlocal:            101 ave         101 max         101 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 316
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.46 | 14.46 | 14.46 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         101   0.00040336839  0.0004201754   0.00059603372  0.0062799915 
+      5100         101   0.50875292     0.024627213    0.027979777    0.043304086  
+      5200         100   0.53008058     0.041756815    0.048966009    0.047686735  
+      5300          98   0.54573932     0.047587469    0.050589616    0.054698345  
+      5400          96   0.56298631     0.054644174    0.054027217    0.045493245  
+      5500          95   0.57287609     0.059325259    0.055248236    0.043563479  
+      5600          93   0.58423645     0.059530387    0.056366577    0.040145791  
+      5700          91   0.59865852     0.062420779    0.056809158    0.037116377  
+      5800          89   0.61220228     0.063841923    0.057610838    0.035162186  
+      5900          87   0.62685381     0.06583351     0.056892184    0.034659058  
+      6000          86   0.6383021      0.070920972    0.058088505    0.03486336   
+      6100          84   0.65594494     0.075093047    0.058543375    0.034741127  
+      6200          84   0.65759722     0.076828979    0.05964225     0.036265031  
+      6300          83   0.66157421     0.073564176    0.055874563    0.040959156  
+      6400          82   0.67106739     0.075914013    0.057132328    0.038400386  
+      6500          81   0.68057943     0.07809572     0.058494303    0.034600654  
+      6600          79   0.69621408     0.07829214     0.057976675    0.035058869  
+      6700          78   0.70377647     0.077804224    0.058088397    0.038570546  
+      6800          77   0.71354031     0.07941644     0.058766697    0.034276567  
+      6900          76   0.72197425     0.079394214    0.058784258    0.034803257  
+      7000          75   0.73118782     0.079954558    0.059615263    0.034182143  
+      7100          75   0.72981832     0.078506803    0.05933558     0.034746017  
+      7200          72   0.75541855     0.076472198    0.058788685    0.033595767  
+      7300          72   0.75545654     0.076512465    0.060371489    0.033716345  
+      7400          69   0.78563876     0.076755562    0.059327807    0.033982311  
+      7500          68   0.79478883     0.075234477    0.059390055    0.033278783  
+      7600          67   0.80394304     0.07337357     0.059151161    0.033764065  
+      7700          67   0.80590143     0.075458302    0.061414582    0.033219177  
+      7800          65   0.82842488     0.075135213    0.059275109    0.03345934   
+      7900          65   0.82992882     0.076739415    0.061358441    0.033045562  
+      8000          62   0.86439786     0.073985787    0.059248708    0.033855494  
+      8100          62   0.86231796     0.071759931    0.059259629    0.032472112  
+      8200          61   0.8768865      0.073251975    0.060469603    0.032336147  
+      8300          59   0.90112575     0.069522479    0.057069294    0.032903788  
+      8400          59   0.90437569     0.073013162    0.060177807    0.032348013  
+      8500          57   0.93513558     0.074163712    0.059868166    0.032129973  
+      8600          56   0.94945182     0.072720987    0.058615804    0.032069723  
+      8700          56   0.94894667     0.07217622     0.0599554      0.031951699  
+      8800          54   0.97951321     0.069451442    0.057486662    0.031861026  
+      8900          53   0.99694312     0.06937422     0.058169881    0.031923553  
+      9000          53   0.9968891      0.069315702    0.057560401    0.031752405  
+      9100          52   1.0151319      0.069375485    0.058181024    0.031774505  
+      9200          52   1.0168478      0.07123737     0.060030802    0.031503493  
+      9300          49   1.0746945      0.069869448    0.058516763    0.031349844  
+      9400          49   1.075198       0.070418696    0.060725237    0.031449699  
+      9500          47   1.1172104      0.068585698    0.059246205    0.031836843  
+      9600          46   1.1392904      0.067243632    0.059489817    0.031042279  
+      9700          45   1.1649854      0.068707001    0.060999207    0.031015205  
+      9800          43   1.2167339      0.068203742    0.061864334    0.030892294  
+      9900          43   1.2179414      0.069538363    0.06395        0.030734812  
+     10000          41   1.2744025      0.068472776    0.060561254    0.030541866  
+Loop time of 0.232249 on 1 procs for 5000 steps with 41 atoms
+
+Performance: 9300376.988 tau/day, 21528.650 timesteps/s, 882.675 katom-step/s
+91.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.023171   | 0.023171   | 0.023171   |   0.0 |  9.98
+Neigh   | 0.0045423  | 0.0045423  | 0.0045423  |   0.0 |  1.96
+Comm    | 0.00042716 | 0.00042716 | 0.00042716 |   0.0 |  0.18
+Output  | 0.19148    | 0.19148    | 0.19148    |   0.0 | 82.45
+Modify  | 0.011612   | 0.011612   | 0.011612   |   0.0 |  5.00
+Other   |            | 0.001015   |            |       |  0.44
+
+Nlocal:             41 ave          41 max          41 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 177
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  37 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.59 | 13.59 | 13.59 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          41   0.061625498    0.068472776    0.060561254    0.00305615   
+     10100          41   0.025254975    0.028061083    0.02437217     0.0026271027 
+     10200          41   0.024393819    0.027104244    0.024633818    0.0023572228 
+     10300          41   0.018015247    0.020016941    0.020621857    0.0025463576 
+     10400          41   0.016921985    0.018802206    0.019360302    0.002082466  
+     10500          41   0.017216494    0.019129438    0.020155469    0.0035436475 
+     10600          41   0.017117386    0.019019318    0.020924624    0.0023704974 
+     10700          40   0.021267544    0.02369812     0.024093057    0.0021665516 
+     10800          39   0.015508579    0.017333117    0.021041382    0.0035660594 
+     10900          39   0.016186792    0.018091121    0.021210051    0.0049345099 
+     11000          39   0.015586494    0.017420199    0.021501559    0.0066808766 
+     11100          39   0.015237777    0.017030457    0.021978242    0.0086073747 
+     11200          39   0.015017416    0.01678417     0.022681353    0.010166477  
+     11300          38   0.014479106    0.016234149    0.02222806     0.0031557802 
+     11400          37   0.012297958    0.013835203    0.019989987    0.0035252488 
+     11500          37   0.011651281    0.013107691    0.018961461    0.0048320998 
+     11600          37   0.012189837    0.013713567    0.018403018    0.0031834233 
+     11700          37   0.013518866    0.015208724    0.019515786    0.0030171621 
+     11800          37   0.014068788    0.015827387    0.019973791    0.0027304961 
+     11900          36   0.014538719    0.016414683    0.02028204     0.0026138589 
+     12000          36   0.012354838    0.013949011    0.019563627    0.0026647531 
+     12100          36   0.011956063    0.013498781    0.019967097    0.0025670349 
+     12200          36   0.012105695    0.013667721    0.020808445    0.0025063398 
+     12300          36   0.011549787    0.013040082    0.020878749    0.0024496418 
+     12400          36   0.010916934    0.012325571    0.019643795    0.004250323  
+     12500          36   0.01099958     0.01241888     0.018388921    0.0030752436 
+     12600          35   0.01033081     0.011708251    0.0179885      0.0035106808 
+     12700          33   0.010252951    0.011717658    0.018411045    0.0017976941 
+     12800          33   0.010678308    0.012203781    0.018558424    0.0017002514 
+     12900          33   0.012180086    0.013920098    0.019432831    0.0016688176 
+     13000          33   0.012765778    0.014589461    0.01998997     0.0016190035 
+     13100          32   0.01043512     0.011981064    0.019750714    0.0029022131 
+     13200          32   0.010106579    0.01160385     0.020095193    0.0019861957 
+     13300          32   0.0094852076   0.010890424    0.018092232    0.0014489801 
+     13400          32   0.011412523    0.013103268    0.01899248     0.0015058469 
+     13500          32   0.011112517    0.012758816    0.018541066    0.0014848955 
+     13600          32   0.010360586    0.011895488    0.018432274    0.0016690155 
+     13700          31   0.010168751    0.011733175    0.01927511     0.0016244377 
+     13800          31   0.010530591    0.012150682    0.018986129    0.0017266198 
+     13900          31   0.011341167    0.013085962    0.020244225    0.0031594327 
+     14000          31   0.011494293    0.013262645    0.020691111    0.0019101224 
+     14100          30   0.010977116    0.012733454    0.021066603    0.0020312424 
+     14200          30   0.011736458    0.013614291    0.021384554    0.0022223346 
+     14300          30   0.013796587    0.016004041    0.023690516    0.0024110671 
+     14400          30   0.011576033    0.013428198    0.02268796     0.0026057617 
+     14500          30   0.011909707    0.01381526     0.022250886    0.0028914407 
+     14600          30   0.011101515    0.012877757    0.022754479    0.0031889992 
+     14700          30   0.011283031    0.013088316    0.019956387    0.0060874479 
+     14800          30   0.010284956    0.011930549    0.016686898    0.0039975609 
+     14900          29   0.0098722494   0.011517624    0.016896924    0.0042842018 
+     15000          29   0.010186166    0.01188386     0.017283688    0.0023888604 
+Loop time of 0.178922 on 1 procs for 5000 steps with 29 atoms
+
+Performance: 12072269.029 tau/day, 27945.067 timesteps/s, 810.407 katom-step/s
+93.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.010314   | 0.010314   | 0.010314   |   0.0 |  5.76
+Neigh   | 0.00091559 | 0.00091559 | 0.00091559 |   0.0 |  0.51
+Comm    | 0.00033777 | 0.00033777 | 0.00033777 |   0.0 |  0.19
+Output  | 0.16153    | 0.16153    | 0.16153    |   0.0 | 90.28
+Modify  | 0.005108   | 0.005108   | 0.005108   |   0.0 |  2.85
+Other   |            | 0.0007212  |            |       |  0.40
+
+Nlocal:             29 ave          29 max          29 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 85
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.data.g++.4

@@ -0,0 +1,358 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tri
+Reading data file ...
+  orthogonal box = (-7 -7 0) to (7 7 9)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  4 atoms
+  4 triangles
+  read_data CPU = 0.001 seconds
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.22 | 13.31 | 13.35 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95089817     1.0393538      0.51608705     0.025335722  
+       600          48   0.83949391     0.91758637     0.46172806     0.022515854  
+       700          48   0.86005308     0.94005801     0.48253125     0.046343793  
+       800          48   0.72552803     0.79301901     0.42419502     0.025365668  
+       900          72   0.67712128     0.71754643     0.37612664     0.028045273  
+      1000          72   0.6037807      0.63982731     0.33903623     0.041568668  
+      1100          72   0.59554924     0.63110442     0.33510774     0.025787354  
+      1200          72   0.59369488     0.62913935     0.33709563     0.037109269  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.42565485     0.44522519     0.24749442     0.052168093  
+      1400          92   0.4636093      0.48492467     0.26417441     0.025118983  
+      1500          92   0.50428332     0.52746876     0.28211978     0.04086654   
+      1600          92   0.4041216      0.42270191     0.24000159     0.026740854  
+      1700         104   0.36993966     0.38488672     0.21498681     0.023950469  
+      1800         104   0.29176495     0.30355343     0.17303905     0.036349423  
+      1900         104   0.26818726     0.27902311     0.15811563     0.024948564  
+      2000         104   0.22279005     0.23179167     0.13346813     0.017280723  
+      2100         104   0.23896556     0.24862073     0.13823816     0.03009918   
+      2200         104   0.20579383     0.21410874     0.12418163     0.039450328  
+      2300         102   0.10971799     0.11424244     0.074956004    0.014807641  
+      2400         102   0.045535097    0.047412833    0.037654864    0.0091413578 
+      2500         102   0.041051596    0.042744445    0.033622408    0.007698999  
+      2600         101   0.034630799    0.036073749    0.027794815    0.0085144929 
+      2700         101   0.025424625    0.026483984    0.020798186    0.006898332  
+      2800         101   0.024152242    0.025158586    0.019868593    0.0095314436 
+      2900         101   0.019076346    0.019871194    0.015184613    0.0068694951 
+      3000         101   0.01182021     0.012312718    0.010833281    0.0078407026 
+      3100         101   0.012007088    0.012507383    0.010192679    0.0072865968 
+      3200         101   0.0065271825   0.0067991484   0.006055543    0.0072082329 
+      3300         101   0.0058659423   0.0061103565   0.005503418    0.0083020848 
+      3400         101   0.0050225565   0.0052318297   0.0045274567   0.0086905727 
+      3500         101   0.0047226341   0.0049194105   0.0041284178   0.0072114544 
+      3600         101   0.0036076755   0.0037579954   0.0035078554   0.0081392066 
+      3700         101   0.0026516472   0.0027621325   0.002544652    0.0076094455 
+      3800         101   0.0021356055   0.0022245891   0.0020628496   0.0068722982 
+      3900         101   0.0014543486   0.0015149465   0.0015027038   0.007022525  
+      4000         101   0.0013476069   0.0014037572   0.0014390136   0.0071511001 
+      4100         101   0.0010740847   0.0011188382   0.0011534394   0.0078442138 
+      4200         101   0.00076777395  0.00079976453  0.00088763722  0.0074201133 
+      4300         101   0.00064877768  0.00067581008  0.00079214623  0.0069999369 
+      4400         101   0.00056602566  0.00058961006  0.00072970843  0.007172149  
+      4500         101   0.00053185285  0.00055401339  0.00069002888  0.0069006923 
+      4600         101   0.00050396242  0.00052496086  0.00064231206  0.0072831983 
+      4700         101   0.0004939245   0.00051450468  0.00060406261  0.0070274519 
+      4800         101   0.0005067638   0.00052787896  0.0006169584   0.0070252715 
+      4900         101   0.00052450136  0.00054635559  0.00063954044  0.0072613866 
+      5000         101   0.00050238069  0.00052331322  0.00063381206  0.0069923836 
+Loop time of 0.392406 on 4 procs for 5000 steps with 101 atoms
+
+Performance: 5504500.640 tau/day, 12741.900 timesteps/s, 1.287 Matom-step/s
+92.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0088673  | 0.0099705  | 0.011728   |   1.1 |  2.54
+Neigh   | 0.0031608  | 0.0036162  | 0.0040394  |   0.6 |  0.92
+Comm    | 0.054781   | 0.057437   | 0.058874   |   0.7 | 14.64
+Output  | 0.16517    | 0.21896    | 0.30823    |  12.1 | 55.80
+Modify  | 0.0072728  | 0.012748   | 0.017229   |   3.4 |  3.25
+Other   |            | 0.08968    |            |       | 22.85
+
+Nlocal:          25.25 ave          28 max          22 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost:          75.75 ave          79 max          73 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 318
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         101   0.00050238069  0.00052331322  0.00063381206  0.0070211922 
+      5100         101   0.51237625     0.028401515    0.030266651    0.047542004  
+      5200         100   0.53673032     0.04868655     0.049607418    0.055178994  
+      5300          98   0.55292145     0.055078502    0.054320412    0.065743408  
+      5400          96   0.56573073     0.057509231    0.056214468    0.04620782   
+      5500          96   0.56811314     0.059996355    0.057130583    0.041366241  
+      5600          92   0.58870851     0.058176956    0.055483365    0.040151041  
+      5700          91   0.59838575     0.062135324    0.056268619    0.037139977  
+      5800          89   0.61367863     0.065388569    0.057599642    0.035611958  
+      5900          88   0.62085434     0.066304196    0.057559466    0.034950213  
+      6000          87   0.62587378     0.064805675    0.056790087    0.036237838  
+      6100          85   0.63938829     0.064969208    0.056078027    0.03552132   
+      6200          83   0.65494135     0.066591169    0.056101931    0.034630474  
+      6300          81   0.66937986     0.066306701    0.054800504    0.034254483  
+      6400          81   0.67013145     0.067097853    0.055854961    0.034280111  
+      6500          80   0.6790132      0.068412844    0.056881014    0.034168381  
+      6600          79   0.68653549     0.06809039     0.056811154    0.033908702  
+      6700          77   0.70162795     0.066842288    0.0557967      0.033646478  
+      6800          75   0.71971093     0.067821847    0.056078774    0.033676107  
+      6900          74   0.72884997     0.068043023    0.055750401    0.034214913  
+      7000          73   0.741055       0.071248239    0.056787992    0.03344658   
+      7100          72   0.74990496     0.070629438    0.056007771    0.034272951  
+      7200          72   0.75147603     0.072294312    0.056870005    0.038376687  
+      7300          72   0.75152274     0.072343811    0.056800621    0.036036623  
+      7400          71   0.75947474     0.07048716     0.055972299    0.033629299  
+      7500          71   0.75927782     0.070278301    0.056900836    0.035271538  
+      7600          70   0.76561822     0.066408884    0.05617217     0.034045712  
+      7700          69   0.77597683     0.06648976     0.056700483    0.033062367  
+      7800          68   0.78867052     0.0687277      0.057387071    0.033095475  
+      7900          67   0.80092333     0.070159036    0.05640023     0.033074777  
+      8000          67   0.80387029     0.073296119    0.058852783    0.033191582  
+      8100          65   0.82162062     0.06787734     0.055167603    0.033911489  
+      8200          65   0.82293648     0.069280915    0.056928499    0.033131095  
+      8300          65   0.82622622     0.072789973    0.059906755    0.033023193  
+      8400          64   0.83807443     0.072671352    0.059696501    0.032696187  
+      8500          61   0.87561225     0.071886699    0.058404764    0.032601058  
+      8600          60   0.89224473     0.075115625    0.060760389    0.032549248  
+      8700          59   0.90437315     0.07301043     0.059680393    0.032331418  
+      8800          58   0.91714907     0.071064475    0.058706043    0.032560687  
+      8900          57   0.92841364     0.066924696    0.055655891    0.031963982  
+      9000          57   0.92657837     0.06494825     0.054846157    0.033987254  
+      9100          56   0.9393931      0.06187335     0.053192019    0.031830438  
+      9200          56   0.93662367     0.058886707    0.052423801    0.031638974  
+      9300          54   0.96949771     0.058618351    0.052230775    0.031585169  
+      9400          53   0.98617614     0.057709997    0.0521297      0.031462885  
+      9500          51   1.0212882      0.055507166    0.050820997    0.032864583  
+      9600          51   1.0207295      0.054899953    0.051106966    0.031197632  
+      9700          50   1.038825       0.053141062    0.049809936    0.031128803  
+      9800          49   1.0578379      0.051480469    0.049706571    0.030966982  
+      9900          48   1.0765858      0.048568721    0.048413084    0.03077346   
+     10000          47   1.0969026      0.046343845    0.048238812    0.03067878   
+Loop time of 0.339694 on 4 procs for 5000 steps with 47 atoms
+
+Performance: 6358664.007 tau/day, 14719.130 timesteps/s, 691.799 katom-step/s
+91.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0082697  | 0.0094229  | 0.010636   |   0.9 |  2.77
+Neigh   | 0.0019222  | 0.0021332  | 0.0024003  |   0.4 |  0.63
+Comm    | 0.046669   | 0.047767   | 0.048681   |   0.4 | 14.06
+Output  | 0.15506    | 0.20052    | 0.26834    |  10.0 | 59.03
+Modify  | 0.005961   | 0.0062645  | 0.0066545  |   0.3 |  1.84
+Other   |            | 0.07358    |            |       | 21.66
+
+Nlocal:          11.75 ave          16 max           4 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost:          35.25 ave          43 max          31 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 202
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  43 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.72 | 13.72 | 13.72 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          47   0.042313945    0.046343845    0.048238812    0.0031829588 
+     10100          47   0.015301196    0.016758453    0.01709909     0.0049007033 
+     10200          47   0.013907369    0.015231881    0.017012208    0.0058822354 
+     10300          47   0.013076355    0.014321722    0.016878308    0.0063771178 
+     10400          47   0.013069713    0.014314447    0.017129868    0.0060544053 
+     10500          47   0.013549117    0.014839509    0.017316811    0.005038037  
+     10600          47   0.013439802    0.014719784    0.016885021    0.0042156468 
+     10700          47   0.011220771    0.012289416    0.015233623    0.0036441984 
+     10800          47   0.0099814505   0.010932065    0.014522881    0.0034799639 
+     10900          47   0.0096058179   0.010520658    0.014440913    0.0032337466 
+     11000          47   0.0083387227   0.0091328868   0.013671791    0.003109424  
+     11100          47   0.0093896494   0.010283902    0.013648072    0.0026934542 
+     11200          46   0.0080569563   0.0088430008   0.013494558    0.0033227229 
+     11300          46   0.0079433758   0.0087183393   0.013255582    0.0025017595 
+     11400          46   0.0082131053   0.0090143839   0.013432928    0.0025609831 
+     11500          46   0.0086708201   0.0095167538   0.0140237      0.0048787265 
+     11600          46   0.0068122941   0.0074769082   0.011927673    0.0064488339 
+     11700          46   0.0075227623   0.0082566903   0.012110115    0.0042416942 
+     11800          45   0.0072330348   0.0079563383   0.012267136    0.0034048479 
+     11900          44   0.0072351925   0.0079772635   0.012364777    0.0025564778 
+     12000          44   0.0069667862   0.0076813283   0.012063595    0.0026245318 
+     12100          44   0.0070363862   0.0077580669   0.01235331     0.0040962445 
+     12200          44   0.0070332478   0.0077546066   0.012391507    0.0040855196 
+     12300          43   0.006888974    0.0076141292   0.01250944     0.0032413632 
+     12400          43   0.0069726667   0.0077066316   0.012649713    0.0053382533 
+     12500          43   0.0084380379   0.0093262524   0.013612524    0.0040338939 
+     12600          41   0.0068380013   0.0075977792   0.012812732    0.0032899814 
+     12700          41   0.0073912915   0.0082125461   0.013194281    0.0046187658 
+     12800          41   0.0081089876   0.0090099862   0.014216855    0.0035891381 
+     12900          40   0.0079216998   0.0088270369   0.014373218    0.0037144356 
+     13000          40   0.0066515495   0.0074117266   0.014238377    0.003842598  
+     13100          39   0.0065633538   0.007335513    0.014863135    0.0038943632 
+     13200          39   0.0066950581   0.0074827119   0.015448367    0.004147601  
+     13300          38   0.0067769957   0.0075984497   0.016038254    0.004422378  
+     13400          38   0.0075957494   0.0085164463   0.017271275    0.004346174  
+     13500          38   0.0079577895   0.0089223701   0.018006278    0.0045246956 
+     13600          37   0.0057787234   0.0065010639   0.017799567    0.0047590682 
+     13700          37   0.0060842787   0.0068448136   0.017273992    0.0049302253 
+     13800          36   0.0054766062   0.0061832651   0.017043555    0.0052192413 
+     13900          36   0.0054552953   0.0061592043   0.01759785     0.0055798708 
+     14000          36   0.0054767411   0.0061834173   0.01795293     0.0072478689 
+     14100          36   0.0057198764   0.0064579249   0.019177836    0.0065582726 
+     14200          36   0.0063731636   0.0071955072   0.020493009    0.007028962  
+     14300          36   0.0082497676   0.0093142538   0.022414624    0.0076449222 
+     14400          36   0.0054945561   0.006203531    0.021312077    0.0095624124 
+     14500          36   0.00573652     0.0064767161   0.021201397    0.011575878  
+     14600          36   0.0064174036   0.0072454556   0.022562059    0.01404045   
+     14700          35   0.0064045224   0.0072584588   0.023705187    0.011526214  
+     14800          35   0.0064474362   0.0073070944   0.024537942    0.013286468  
+     14900          35   0.007220356    0.0081830702   0.025671819    0.015672233  
+     15000          34   0.0063783086   0.0072580753   0.019282966    0.0091892427 
+Loop time of 0.288741 on 4 procs for 5000 steps with 34 atoms
+
+Performance: 7480745.885 tau/day, 17316.541 timesteps/s, 588.762 katom-step/s
+94.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0024909  | 0.0048816  | 0.0063741  |   2.2 |  1.69
+Neigh   | 0.00027783 | 0.00047397 | 0.00057846 |   0.0 |  0.16
+Comm    | 0.029395   | 0.031811   | 0.033792   |   0.9 | 11.02
+Output  | 0.14606    | 0.18368    | 0.24324    |   9.1 | 63.61
+Modify  | 0.0016781  | 0.0030068  | 0.0034538  |   1.4 |  1.04
+Other   |            | 0.06489    |            |       | 22.47
+
+Nlocal:            8.5 ave          13 max           4 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:           25.5 ave          30 max          21 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 75
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/gransurf/log.1Jul24.tri.gran.global.g++.1

@@ -0,0 +1,326 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tri
+Read molecule template tris:
+LAMMPS data file for tri plane
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  4 triangles with 5 points
+
+fix             20 all surface/global tris hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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 = 22 22 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.802 | 5.802 | 5.802 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+       100          24   0.43156905     0.43156905     0.21119336     0.005627034  
+       200          24   0.73291569     0.73291569     0.35866087     0.009556157  
+       300          24   1.125323       1.125323       0.55068998     0.014672579  
+       400          24   1.608791       1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          44   1.0393538      1.0393538      0.51608705     0.025335722  
+       600          44   0.91758637     0.91758637     0.46172806     0.022367468  
+       700          44   0.94006427     0.94006427     0.48254195     0.035377091  
+       800          44   0.79393033     0.79393033     0.42561821     0.019944664  
+       900          68   0.72089876     0.72089876     0.37868178     0.027381075  
+      1000          68   0.63399342     0.63399342     0.33666552     0.052128303  
+      1100          68   0.63724402     0.63724402     0.3383098      0.024876228  
+      1200          68   0.61528554     0.61528554     0.33134629     0.030248652  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          88   0.45289831     0.45289831     0.24603739     0.032314185  
+      1400          88   0.51028258     0.51028258     0.27462447     0.027721293  
+      1500          88   0.52728648     0.52728648     0.28580371     0.030249652  
+      1600          88   0.46373765     0.46373765     0.25474076     0.023383063  
+      1700         100   0.32521568     0.32521568     0.18562847     0.044525946  
+      1800         100   0.30850324     0.30850324     0.17882757     0.031769348  
+      1900         100   0.25365045     0.25365045     0.15147723     0.020592523  
+      2000         100   0.21618068     0.21618068     0.12797228     0.016906763  
+      2100         100   0.24765667     0.24765667     0.13878326     0.014412505  
+      2200         100   0.23385635     0.23385635     0.13254109     0.028043795  
+      2300          99   0.11484142     0.11484142     0.071915879    0.013339994  
+      2400          99   0.053909031    0.053909031    0.042287371    0.0035097518 
+      2500          99   0.042127087    0.042127087    0.032805292    0.0034968993 
+      2600          98   0.036200554    0.036200554    0.027643964    0.0031738712 
+      2700          98   0.030498126    0.030498126    0.02276547     0.0062463557 
+      2800          98   0.025833054    0.025833054    0.019565401    0.0016975051 
+      2900          98   0.020275355    0.020275355    0.015121787    0.0039809964 
+      3000          97   0.011459209    0.011459209    0.0095066644   0.00078861732
+      3100          97   0.011129563    0.011129563    0.0090167087   0.0011316298 
+      3200          97   0.008702876    0.008702876    0.006583492    0.0019280113 
+      3300          97   0.0049159683   0.0049159683   0.0043967355   0.0005341051 
+      3400          97   0.003181781    0.003181781    0.0029259249   0.0004882333 
+      3500          97   0.0026088972   0.0026088972   0.002409282    0.0014155092 
+      3600          96   0.0022479435   0.0022479435   0.0021341332   0.00038317544
+      3700          96   0.0020120096   0.0020120096   0.0019144129   0.00030490152
+      3800          96   0.0016420292   0.0016420292   0.0016430538   0.00060824148
+      3900          96   0.0015381905   0.0015381905   0.0016050403   0.00025407021
+      4000          96   0.0013553693   0.0013553693   0.0014834876   0.001040242  
+      4100          96   0.0013261679   0.0013261679   0.0015039405   0.00015428329
+      4200          96   0.0013369471   0.0013369471   0.0015527737   0.00015511402
+      4300          96   0.001244062    0.001244062    0.0014317602   0.00023157907
+      4400          96   0.00093908982  0.00093908982  0.0010831596   0.00085817995
+      4500          96   0.00088407737  0.00088407737  0.0010577616   0.00028165751
+      4600          96   0.0007048497   0.0007048497   0.00089917743  0.00018721659
+      4700          96   0.00070321437  0.00070321437  0.00093327157  0.00027581655
+      4800          96   0.00069636212  0.00069636212  0.00095998895  0.00026832587
+      4900          96   0.00066716522  0.00066716522  0.00098882541  0.00024920816
+      5000          96   0.00063786253  0.00063786253  0.00084144507  0.0006959824 
+Loop time of 0.268261 on 1 procs for 5000 steps with 96 atoms
+
+Performance: 8051852.379 tau/day, 18638.547 timesteps/s, 1.789 Matom-step/s
+97.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0036514  | 0.0036514  | 0.0036514  |   0.0 |  1.36
+Neigh   | 0.0038871  | 0.0038871  | 0.0038871  |   0.0 |  1.45
+Comm    | 0.00039419 | 0.00039419 | 0.00039419 |   0.0 |  0.15
+Output  | 0.22313    | 0.22313    | 0.22313    |   0.0 | 83.18
+Modify  | 0.035998   | 0.035998   | 0.035998   |   0.0 | 13.42
+Other   |            | 0.001202   |            |       |  0.45
+
+Nlocal:             96 ave          96 max          96 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:            148 ave         148 max         148 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148
+Ave neighs/atom = 1.5416667
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.62 | 10.62 | 10.62 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000          96   0.00063786253  0.00063786253  0.00084144507  0.00068409102
+      5100          96   0.028313992    0.028313992    0.02867394     0.0064318866 
+      5200          94   0.039240682    0.039240682    0.046630048    0.0021250045 
+      5300          94   0.045894493    0.045894493    0.051041657    0.004288554  
+      5400          90   0.046049624    0.046049624    0.052748479    0.0023413632 
+      5500          89   0.044619749    0.044619749    0.051759567    0.0025268066 
+      5600          87   0.046502592    0.046502592    0.052805904    0.0022671331 
+      5700          86   0.047502773    0.047502773    0.052890192    0.0025018431 
+      5800          83   0.049317538    0.049317538    0.052470227    0.0024522166 
+      5900          81   0.051463883    0.051463883    0.053324316    0.0024303621 
+      6000          79   0.052996121    0.052996121    0.054122681    0.0024352971 
+      6100          78   0.048074683    0.048074683    0.051044879    0.0020985852 
+      6200          75   0.04840275     0.04840275     0.049998948    0.0020567512 
+      6300          74   0.048896993    0.048896993    0.05012768     0.0020235986 
+      6400          72   0.048661741    0.048661741    0.047914934    0.0027397448 
+      6500          72   0.049815101    0.049815101    0.04823434     0.0022998212 
+      6600          72   0.050578127    0.050578127    0.047972859    0.0023500543 
+      6700          71   0.053700957    0.053700957    0.049203548    0.0021231176 
+      6800          70   0.054955705    0.054955705    0.048252513    0.0022219662 
+      6900          69   0.055089911    0.055089911    0.048327243    0.0021431702 
+      7000          68   0.054713581    0.054713581    0.047461258    0.0027194558 
+      7100          68   0.055154516    0.055154516    0.048042367    0.0020996652 
+      7200          68   0.052688949    0.052688949    0.047223673    0.0031629618 
+      7300          66   0.053031698    0.053031698    0.046492962    0.0020164648 
+      7400          66   0.053814798    0.053814798    0.048105161    0.0019830573 
+      7500          64   0.050060478    0.050060478    0.046862322    0.0017880464 
+      7600          63   0.051383282    0.051383282    0.047500425    0.0018639548 
+      7700          61   0.047761405    0.047761405    0.045091014    0.001632776  
+      7800          60   0.047463305    0.047463305    0.045176189    0.001591933  
+      7900          60   0.048347642    0.048347642    0.046537806    0.0016308357 
+      8000          58   0.04714196     0.04714196     0.045527272    0.0015641403 
+      8100          58   0.046968881    0.046968881    0.04598277     0.0024094931 
+      8200          57   0.046997734    0.046997734    0.045676536    0.0014922033 
+      8300          57   0.045562254    0.045562254    0.045872476    0.0014466327 
+      8400          55   0.044408194    0.044408194    0.045223172    0.0013596468 
+      8500          55   0.043334554    0.043334554    0.045957536    0.0013267805 
+      8600          52   0.0407858      0.0407858      0.043378073    0.0011793941 
+      8700          52   0.039828276    0.039828276    0.043948609    0.0014514912 
+      8800          50   0.038530301    0.038530301    0.043112182    0.0010705032 
+      8900          50   0.038936121    0.038936121    0.044360368    0.0010817763 
+      9000          49   0.038340922    0.038340922    0.043586145    0.0010435081 
+      9100          48   0.037704467    0.037704467    0.043398687    0.0010047485 
+      9200          48   0.039439971    0.039439971    0.045446967    0.0010509895 
+      9300          48   0.040146494    0.040146494    0.047222767    0.0010698143 
+      9400          46   0.036196314    0.036196314    0.04514472     0.00092352701
+      9500          44   0.035428166    0.035428166    0.043156558    0.00086370075
+      9600          44   0.036236057    0.036236057    0.045015316    0.00088339425
+      9700          43   0.033612512    0.033612512    0.042808614    0.0008003869 
+      9800          42   0.034119077    0.034119077    0.043448026    0.0007931345 
+      9900          41   0.033534569    0.033534569    0.04281968     0.00076053851
+     10000          40   0.032867612    0.032867612    0.041673148    0.00072678237
+Loop time of 0.246836 on 1 procs for 5000 steps with 40 atoms
+
+Performance: 8750744.841 tau/day, 20256.354 timesteps/s, 810.254 katom-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    | 0.0022158  | 0.0022158  | 0.0022158  |   0.0 |  0.90
+Neigh   | 0.0032745  | 0.0032745  | 0.0032745  |   0.0 |  1.33
+Comm    | 0.0003966  | 0.0003966  | 0.0003966  |   0.0 |  0.16
+Output  | 0.20971    | 0.20971    | 0.20971    |   0.0 | 84.96
+Modify  | 0.030201   | 0.030201   | 0.030201   |   0.0 | 12.24
+Other   |            | 0.001038   |            |       |  0.42
+
+Nlocal:             40 ave          40 max          40 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:             18 ave          18 max          18 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18
+Ave neighs/atom = 0.45
+Neighbor list builds = 333
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.62 | 10.62 | 10.62 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          40   0.032867612    0.032867612    0.041673148    0.00072685327
+     10100          40   0.0076052221   0.0076052221   0.0076988542   0.00016814267
+     10200          40   0.0032668297   0.0032668297   0.0038743591   0.00054487661
+     10300          40   0.003316664    0.003316664    0.0040375473   7.3327605e-05
+     10400          40   0.0030064853   0.0030064853   0.0039975834   6.6469913e-05
+     10500          40   0.0030342866   0.0030342866   0.004203116    6.7084568e-05
+     10600          40   0.0030020199   0.0030020199   0.0043687727   6.6371188e-05
+     10700          40   0.0027999261   0.0027999261   0.003947504    0.00010754343
+     10800          40   0.0027031744   0.0027031744   0.0038359994   6.3984417e-05
+     10900          40   0.0027373574   0.0027373574   0.0039800535   7.0481083e-05
+     11000          39   0.0029362062   0.0029362062   0.002978473    6.9069963e-05
+     11100          39   0.0037840086   0.0037840086   0.0036639284   8.1514925e-05
+     11200          39   0.0045558771   0.0045558771   0.0041248127   9.8142478e-05
+     11300          39   0.0017981927   0.0017981927   0.0025146205   0.00031779839
+     11400          39   0.0016431107   0.0016431107   0.0024756094   4.4978596e-05
+     11500          39   0.0017504997   0.0017504997   0.0026753481   4.7200446e-05
+     11600          39   0.0020008726   0.0020008726   0.0029721732   5.2678933e-05
+     11700          39   0.0014870059   0.0014870059   0.0026506345   4.152681e-05 
+     11800          39   0.0016074438   0.0016074438   0.002888528   -3.0912602e-05
+     11900          39   0.0017722588   0.0017722588   0.0031282687   4.1702851e-05
+     12000          39   0.0027430864   0.0027430864   0.0039301824   6.8654618e-05
+     12100          39   0.0031883241   0.0031883241   0.0041806787   7.8260758e-05
+     12200          38   0.0013269284   0.0013269284   0.0032322246   3.6635105e-05
+     12300          38   0.0016569097   0.0016569097   0.0036433609   0.00041718571
+     12400          38   0.00094008147  0.00094008147  0.0033452514   3.7496272e-05
+     12500          37   0.00095698445  0.00095698445  0.0023073129   3.715434e-05 
+     12600          37   0.00098175769  0.00098175769  0.0025359749   3.7459507e-05
+     12700          37   0.0010099586   0.0010099586   0.0027775856   3.7772603e-05
+     12800          37   0.0010435337   0.0010435337   0.0030319623   3.811889e-05 
+     12900          37   0.0011032701   0.0011032701   0.0032983521   2.3599435e-05
+     13000          37   0.0012957624   0.0012957624   0.003683326    4.2333566e-05
+     13100          37   0.0010512853   0.0010512853   0.0037476793   3.6717097e-05
+     13200          37   0.0010868252   0.0010868252   0.0040740128   0.00018164133
+     13300          37   0.0011180293   0.0011180293   0.0044202397   3.643358e-05 
+     13400          37   0.0011178538   0.0011178538   0.0047516047   3.5746318e-05
+     13500          37   0.0007777481   0.0007777481   0.0037726389   5.3444345e-05
+     13600          36   0.0007999147   0.0007999147   0.003070242    3.248155e-05 
+     13700          36   0.0008389068   0.0008389068   0.003346172    2.9660005e-05
+     13800          36   0.00086583182  0.00086583182  0.0036410575   3.0212331e-05
+     13900          36   0.00058473604  0.00058473604  0.0024273755   5.7952251e-05
+     14000          36   0.00055727478  0.00055727478  0.0019113805   0.00011095694
+     14100          35   0.00044295291  0.00044295291  0.00066952242  0.00050643096
+     14200          35   0.00041514525  0.00041514525  0.00045222556  9.4438091e-05
+     14300          35   0.00042269774  0.00042269774  0.00047195914  4.5343892e-05
+     14400          35   0.00042495865  0.00042495865  0.00049753292  4.5106479e-05
+     14500          35   0.00040895208  0.00040895208  0.00051927404  4.6530808e-05
+     14600          35   0.00039129621  0.00039129621  0.00054194363  0.00019698404
+     14700          35   0.00039266334  0.00039266334  0.00058307961  4.7472072e-05
+     14800          35   0.00040570773  0.00040570773  0.00065710296  4.7982077e-05
+     14900          35   0.00040991932  0.00040991932  0.0007334058   4.8236973e-05
+     15000          35   0.00041469341  0.00041469341  0.00081836212  4.8450505e-05
+Loop time of 0.213298 on 1 procs for 5000 steps with 35 atoms
+
+Performance: 10126681.077 tau/day, 23441.391 timesteps/s, 820.449 katom-step/s
+88.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0012286  | 0.0012286  | 0.0012286  |   0.0 |  0.58
+Neigh   | 0.00025877 | 0.00025877 | 0.00025877 |   0.0 |  0.12
+Comm    | 0.00026642 | 0.00026642 | 0.00026642 |   0.0 |  0.12
+Output  | 0.19361    | 0.19361    | 0.19361    |   0.0 | 90.77
+Modify  | 0.017202   | 0.017202   | 0.017202   |   0.0 |  8.06
+Other   |            | 0.0007333  |            |       |  0.34
+
+Nlocal:             35 ave          35 max          35 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:             26 ave          26 max          26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 26
+Ave neighs/atom = 0.74285714
+Neighbor list builds = 37
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.global.g++.4

@@ -0,0 +1,327 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  2 by 2 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tri
+Read molecule template tris:
+LAMMPS data file for tri plane
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  4 triangles with 5 points
+
+fix             20 all surface/global tris hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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 = 22 22 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.785 | 5.785 | 5.785 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+       100          24   0.43156905     0.43156905     0.21119336     0.005627034  
+       200          24   0.73291569     0.73291569     0.35866087     0.009556157  
+       300          24   1.125323       1.125323       0.55068998     0.014672579  
+       400          24   1.608791       1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          44   1.0393538      1.0393538      0.51608705     0.025335722  
+       600          44   0.91758637     0.91758637     0.46172806     0.022367468  
+       700          44   0.94006427     0.94006427     0.48254195     0.035377091  
+       800          44   0.79393033     0.79393033     0.42561821     0.019944664  
+       900          68   0.72089876     0.72089876     0.37868178     0.027381075  
+      1000          68   0.63399342     0.63399342     0.33666552     0.052128303  
+      1100          68   0.63724402     0.63724402     0.3383098      0.024876228  
+      1200          68   0.61528554     0.61528554     0.33134629     0.030248652  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          88   0.45289831     0.45289831     0.24603739     0.032314185  
+      1400          88   0.51028258     0.51028258     0.27462447     0.027721293  
+      1500          88   0.52728648     0.52728648     0.28580371     0.030249652  
+      1600          88   0.46373765     0.46373765     0.25474076     0.023383063  
+      1700         100   0.32521568     0.32521568     0.18562847     0.044525945  
+      1800         100   0.30850324     0.30850324     0.17882757     0.031769348  
+      1900         100   0.25365045     0.25365045     0.15147723     0.020592523  
+      2000         100   0.21618068     0.21618068     0.12797228     0.016906764  
+      2100         100   0.24765668     0.24765668     0.13878326     0.014412505  
+      2200         100   0.23385636     0.23385636     0.13254109     0.028043759  
+      2300          99   0.11484144     0.11484144     0.07191588     0.013339992  
+      2400          99   0.053908946    0.053908946    0.042287303    0.0035096828 
+      2500          99   0.042127084    0.042127084    0.032805289    0.0034968494 
+      2600          98   0.03620012     0.03620012     0.027643861    0.0031757884 
+      2700          98   0.030497382    0.030497382    0.02276464     0.0062433907 
+      2800          98   0.025840421    0.025840421    0.019571636    0.0017100476 
+      2900          98   0.020282706    0.020282706    0.01512433     0.0039918866 
+      3000          97   0.011469683    0.011469683    0.0095129501   0.00083264863
+      3100          97   0.011061428    0.011061428    0.0089852941   0.0011413524 
+      3200          97   0.0085729018   0.0085729018   0.0065027781   0.0015793608 
+      3300          97   0.0048844117   0.0048844117   0.0043831348   0.00054654825
+      3400          97   0.0031718513   0.0031718513   0.002919676    0.00041030186
+      3500          97   0.0026149541   0.0026149541   0.0024273609   0.00064176505
+      3600          96   0.0022374762   0.0022374762   0.0021346878   0.0009000487 
+      3700          96   0.002015425    0.002015425    0.0019283015   0.00010102156
+      3800          96   0.0016640247   0.0016640247   0.0016542081   0.00058063795
+      3900          96   0.0014953491   0.0014953491   0.0015554014   0.00043366101
+      4000          96   0.0014314643   0.0014314643   0.001549993    0.00016144849
+      4100          96   0.0012797618   0.0012797618   0.001462077    0.0001478758 
+      4200          96   0.001301217    0.001301217    0.0015150334   0.00032745678
+      4300          96   0.0011719389   0.0011719389   0.0013301205   0.00025779628
+      4400          96   0.00092491728  0.00092491728  0.0010319633   0.00030044217
+      4500          96   0.00087292243  0.00087292243  0.001019192    0.00025577747
+      4600          96   0.00075144495  0.00075144495  0.00091990059  0.00018817234
+      4700          96   0.00074883306  0.00074883306  0.00093930259  0.0005619372 
+      4800          96   0.00065460832  0.00065460832  0.00089919023  0.00024621022
+      4900          96   0.0006499224   0.0006499224   0.00092528447  0.00026790153
+      5000          96   0.00061981936  0.00061981936  0.00078233948  0.00061552671
+Loop time of 0.363222 on 4 procs for 5000 steps with 96 atoms
+
+Performance: 5946774.227 tau/day, 13765.681 timesteps/s, 1.322 Matom-step/s
+95.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0013004  | 0.0013955  | 0.0015524  |   0.3 |  0.38
+Neigh   | 0.0014703  | 0.0016933  | 0.0019742  |   0.5 |  0.47
+Comm    | 0.019443   | 0.020106   | 0.020622   |   0.3 |  5.54
+Output  | 0.23038    | 0.26505    | 0.3205     |   7.3 | 72.97
+Modify  | 0.012416   | 0.01734    | 0.02093    |   2.5 |  4.77
+Other   |            | 0.05763    |            |       | 15.87
+
+Nlocal:             24 ave          25 max          22 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:           9.25 ave          12 max           8 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Neighs:          36.25 ave          40 max          34 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 145
+Ave neighs/atom = 1.5104167
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.6 | 10.6 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000          96   0.00061981936  0.00061981936  0.00078233948  0.00061520755
+      5100          96   0.028314129    0.028314129    0.028887614    0.0015596074 
+      5200          93   0.038280284    0.038280284    0.045433502    0.003972808  
+      5300          92   0.044602602    0.044602602    0.050026258    0.0066549492 
+      5400          88   0.043591861    0.043591861    0.050587055    0.0021499387 
+      5500          88   0.043643437    0.043643437    0.051930078    0.0045848219 
+      5600          86   0.044398335    0.044398335    0.050588091    0.0021861193 
+      5700          86   0.048834817    0.048834817    0.052122986    0.0024353201 
+      5800          82   0.048657023    0.048657023    0.050882437    0.0022637024 
+      5900          79   0.047422209    0.047422209    0.050391753    0.0020519953 
+      6000          78   0.047430795    0.047430795    0.050706223    0.0020757537 
+      6100          76   0.047766342    0.047766342    0.050881831    0.0020365653 
+      6200          74   0.048553742    0.048553742    0.049322747    0.0040124193 
+      6300          73   0.050329565    0.050329565    0.050219503    0.0021932369 
+      6400          71   0.049899479    0.049899479    0.047423384    0.0019659021 
+      6500          71   0.051053882    0.051053882    0.048643589    0.0020292656 
+      6600          71   0.051795185    0.051795185    0.04927532     0.0023715227 
+      6700          69   0.052264693    0.052264693    0.048643292    0.0020434717 
+      6800          69   0.052349883    0.052349883    0.049265236    0.0020181077 
+      6900          68   0.051428051    0.051428051    0.048628957    0.0019545319 
+      7000          67   0.050476407    0.050476407    0.048064128    0.0018923271 
+      7100          67   0.050313513    0.050313513    0.048219142    0.001884633  
+      7200          67   0.050521342    0.050521342    0.047963518    0.0021063865 
+      7300          66   0.049017518    0.049017518    0.047288558    0.0018972353 
+      7400          65   0.048690842    0.048690842    0.048162015    0.0017669135 
+      7500          64   0.048934259    0.048934259    0.047906689    0.0019361894 
+      7600          62   0.048293135    0.048293135    0.047386457    0.0023701331 
+      7700          61   0.050821617    0.050821617    0.048266806    0.0018564185 
+      7800          60   0.052493396    0.052493396    0.049727548    0.0017921461 
+      7900          59   0.053162734    0.053162734    0.050327775    0.0017510558 
+      8000          57   0.051249525    0.051249525    0.048540418    0.0028770132 
+      8100          57   0.05261519     0.05261519     0.049923888    0.0016707326 
+      8200          55   0.051727022    0.051727022    0.047928098    0.0014557055 
+      8300          55   0.050489803    0.050489803    0.048163815    0.0033275674 
+      8400          54   0.049599363    0.049599363    0.047431898    0.0015088762 
+      8500          54   0.052050538    0.052050538    0.048908289    0.0015666966 
+      8600          52   0.050340482    0.050340482    0.046440415    0.0014555948 
+      8700          52   0.052028316    0.052028316    0.048176195    0.0015106353 
+      8800          50   0.0499901      0.0499901      0.045788044    0.0025087962 
+      8900          50   0.051750338    0.051750338    0.047753896    0.0014377545 
+      9000          50   0.051966831    0.051966831    0.048823952    0.0014437681 
+      9100          49   0.051660945    0.051660945    0.048110255    0.0014336784 
+      9200          49   0.051126513    0.051126513    0.048962201    0.0014162724 
+      9300          48   0.049057888    0.049057888    0.0492291      0.0013197818 
+      9400          48   0.045030047    0.045030047    0.047529619    0.0013481748 
+      9500          48   0.045513589    0.045513589    0.048536638    0.0012236674 
+      9600          48   0.043665627    0.043665627    0.048296609    0.0011806622 
+      9700          48   0.044106239    0.044106239    0.049540196    0.0011963288 
+      9800          46   0.042160287    0.042160287    0.048481885    0.0011107764 
+      9900          46   0.041772009    0.041772009    0.049483596    0.0011344326 
+     10000          44   0.040236277    0.040236277    0.045816406    0.00099962018
+Loop time of 0.306426 on 4 procs for 5000 steps with 44 atoms
+
+Performance: 7049016.148 tau/day, 16317.167 timesteps/s, 717.955 katom-step/s
+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    | 0.00093851 | 0.00097842 | 0.0010014  |   0.0 |  0.32
+Neigh   | 0.0011773  | 0.0012138  | 0.0012749  |   0.1 |  0.40
+Comm    | 0.012859   | 0.013509   | 0.01418    |   0.5 |  4.41
+Output  | 0.19691    | 0.22604    | 0.2754     |   6.8 | 73.77
+Modify  | 0.0097789  | 0.010556   | 0.011241   |   0.5 |  3.44
+Other   |            | 0.05412    |            |       | 17.66
+
+Nlocal:             11 ave          20 max           4 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost:              4 ave           6 max           2 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:           9.75 ave          23 max           2 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 39
+Ave neighs/atom = 0.88636364
+Neighbor list builds = 333
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.6 | 10.6 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          44   0.040236277    0.040236277    0.045816406    0.00099979881
+     10100          44   0.010977052    0.010977052    0.010149182    0.00026758119
+     10200          44   0.004605352    0.004605352    0.0053045614   0.00011226198
+     10300          44   0.0053942032   0.0053942032   0.0056431085   0.00013149135
+     10400          44   0.0036859511   0.0036859511   0.0041662707   9.2662763e-05
+     10500          44   0.0039184347   0.0039184347   0.0043067155   0.00049979829
+     10600          44   0.0044427233   0.0044427233   0.0045879783   0.00011077625
+     10700          44   0.0029607594   0.0029607594   0.0034776101   0.0006068726 
+     10800          44   0.0026942916   0.0026942916   0.0034401136   6.706354e-05 
+     10900          44   0.0026203469   0.0026203469   0.0034492724   6.9607138e-05
+     11000          44   0.0019864947   0.0019864947   0.0031427116   8.3134017e-06
+     11100          44   0.0019240976   0.0019240976   0.0032808084   2.0347364e-05
+     11200          44   0.0018635948   0.0018635948   0.0034030363   5.7875998e-05
+     11300          44   0.0017686207   0.0017686207   0.0029556669   9.3363224e-05
+     11400          44   0.0014303652   0.0014303652   0.002751691    5.9528496e-05
+     11500          44   0.001399414    0.001399414    0.0027540021   5.8871141e-05
+     11600          44   0.0011285459   0.0011285459   0.0017454672   0.00063103388
+     11700          44   0.0010672518   0.0010672518   0.0014970714   0.00012978783
+     11800          44   0.0010754046   0.0010754046   0.0015525936   0.00011139988
+     11900          44   0.00093155287  0.00093155287  0.0011682302   0.00012515367
+     12000          44   0.00084853622  0.00084853622  0.0010681768   0.00010639935
+     12100          44   0.00069411148  0.00069411148  0.00077780972  7.3742549e-05
+     12200          44   0.0006859885   0.0006859885   0.0007696296   9.3309816e-05
+     12300          44   0.00064103944  0.00064103944  0.00072985388  0.0001474211 
+     12400          44   0.00063849822  0.00063849822  0.00072417306  9.4166534e-05
+     12500          44   0.0006361049   0.0006361049   0.00068646857  9.5282342e-05
+     12600          44   0.00063622199  0.00063622199  0.00068538208  9.5058162e-05
+     12700          44   0.00062165913  0.00062165913  0.00066876644  9.412044e-05 
+     12800          44   0.00058480739  0.00058480739  0.00063172101  0.00018653887
+     12900          44   0.00054058957  0.00054058957  0.00059549487  9.384774e-05 
+     13000          44   0.00051904254  0.00051904254  0.00057073513  9.4434337e-05
+     13100          44   0.00053410816  0.00053410816  0.00057766113  9.61856e-05  
+     13200          44   0.00050156547  0.00050156547  0.00055212122  9.7382505e-05
+     13300          44   0.00049740896  0.00049740896  0.00054826803  9.7690479e-05
+     13400          44   0.00049775099  0.00049775099  0.00054791017  9.7482658e-05
+     13500          44   0.00049205909  0.00049205909  0.00054071132  0.00010353798
+     13600          44   0.00049240333  0.00049240333  0.00054031425  9.7448102e-05
+     13700          44   0.00049274845  0.00049274845  0.00053984708  9.7497469e-05
+     13800          43   0.00050763917  0.00050763917  0.00055870605  8.5113661e-05
+     13900          43   0.00047304434  0.00047304434  0.00054545171  7.7477263e-05
+     14000          43   0.00047307851  0.00047307851  0.00056349029  0.00016615605
+     14100          43   0.00048268391  0.00048268391  0.00059292333  8.4939642e-05
+     14200          43   0.00049712412  0.00049712412  0.00064043909  8.522618e-05 
+     14300          43   0.00051010248  0.00051010248  0.00069557642  8.5161341e-05
+     14400          43   0.0005010299   0.0005010299   0.00074528156  8.5292218e-05
+     14500          43   0.00050900735  0.00050900735  0.00081321917  8.5452422e-05
+     14600          43   0.00051293789  0.00051293789  0.00088464504  8.5523903e-05
+     14700          43   0.00050022161  0.00050022161  0.00094898195  8.520624e-05 
+     14800          43   0.00049641051  0.00049641051  0.0010219267   8.5106195e-05
+     14900          43   0.00048906772  0.00048906772  0.0010926634   8.4926556e-05
+     15000          43   0.00048008443  0.00048008443  0.0011603655   8.470585e-05 
+Loop time of 0.301772 on 4 procs for 5000 steps with 43 atoms
+
+Performance: 7157719.630 tau/day, 16568.795 timesteps/s, 712.458 katom-step/s
+95.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00035986 | 0.00077488 | 0.0011039  |   0.0 |  0.26
+Neigh   | 0.00012595 | 0.00015205 | 0.00018739 |   0.0 |  0.05
+Comm    | 0.0082732  | 0.0097396  | 0.011683   |   1.3 |  3.23
+Output  | 0.19202    | 0.2262     | 0.27636    |   7.0 | 74.96
+Modify  | 0.0029097  | 0.0064286  | 0.01144    |   3.9 |  2.13
+Other   |            | 0.05847    |            |       | 19.38
+
+Nlocal:          10.75 ave          20 max           5 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:              4 ave           7 max           2 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:             10 ave          22 max           2 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 40
+Ave neighs/atom = 0.93023256
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.global.stl.g++.1

@@ -0,0 +1,315 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global surf.tri.stl hooke                 4000.0 NULL 100.0 NULL 0.5 1
+Reading STL object STL version of surf.tri from text file surf.tri.stl
+#fix             20 all surface/global surf.tri.stl hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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 = 22 22 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.802 | 5.802 | 5.802 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+       100          24   0.43156905     0.43156905     0.21119336     0.005627034  
+       200          24   0.73291569     0.73291569     0.35866087     0.009556157  
+       300          24   1.125323       1.125323       0.55068998     0.014672579  
+       400          24   1.608791       1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          44   1.0393538      1.0393538      0.51608705     0.025335722  
+       600          44   0.91758637     0.91758637     0.46172806     0.022367468  
+       700          44   0.94006427     0.94006427     0.48254195     0.035377091  
+       800          44   0.79393033     0.79393033     0.42561821     0.019944664  
+       900          68   0.72089876     0.72089876     0.37868178     0.027381075  
+      1000          68   0.63399342     0.63399342     0.33666552     0.052128303  
+      1100          68   0.63724402     0.63724402     0.3383098      0.024876228  
+      1200          68   0.61528554     0.61528554     0.33134629     0.030248652  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          88   0.45289831     0.45289831     0.24603739     0.032314185  
+      1400          88   0.51028258     0.51028258     0.27462447     0.027721293  
+      1500          88   0.52728648     0.52728648     0.28580371     0.030249652  
+      1600          88   0.46373765     0.46373765     0.25474076     0.023383063  
+      1700         100   0.32521568     0.32521568     0.18562847     0.044525946  
+      1800         100   0.30850324     0.30850324     0.17882757     0.031769348  
+      1900         100   0.25365045     0.25365045     0.15147723     0.020592523  
+      2000         100   0.21618068     0.21618068     0.12797228     0.016906763  
+      2100         100   0.24765667     0.24765667     0.13878326     0.014412505  
+      2200         100   0.23385635     0.23385635     0.13254109     0.028043795  
+      2300          99   0.11484142     0.11484142     0.071915879    0.013339994  
+      2400          99   0.053909031    0.053909031    0.042287371    0.0035097518 
+      2500          99   0.042127087    0.042127087    0.032805292    0.0034968993 
+      2600          98   0.036200554    0.036200554    0.027643964    0.0031738712 
+      2700          98   0.030498126    0.030498126    0.02276547     0.0062463557 
+      2800          98   0.025833054    0.025833054    0.019565401    0.0016975051 
+      2900          98   0.020275355    0.020275355    0.015121787    0.0039809964 
+      3000          97   0.011459209    0.011459209    0.0095066644   0.00078861732
+      3100          97   0.011129563    0.011129563    0.0090167087   0.0011316298 
+      3200          97   0.008702876    0.008702876    0.006583492    0.0019280113 
+      3300          97   0.0049159683   0.0049159683   0.0043967355   0.0005341051 
+      3400          97   0.003181781    0.003181781    0.0029259249   0.0004882333 
+      3500          97   0.0026088972   0.0026088972   0.002409282    0.0014155092 
+      3600          96   0.0022479435   0.0022479435   0.0021341332   0.00038317544
+      3700          96   0.0020120096   0.0020120096   0.0019144129   0.00030490152
+      3800          96   0.0016420292   0.0016420292   0.0016430538   0.00060824148
+      3900          96   0.0015381905   0.0015381905   0.0016050403   0.00025407021
+      4000          96   0.0013553693   0.0013553693   0.0014834876   0.001040242  
+      4100          96   0.0013261679   0.0013261679   0.0015039405   0.00015428329
+      4200          96   0.0013369471   0.0013369471   0.0015527737   0.00015511402
+      4300          96   0.001244062    0.001244062    0.0014317602   0.00023157907
+      4400          96   0.00093908982  0.00093908982  0.0010831596   0.00085817995
+      4500          96   0.00088407737  0.00088407737  0.0010577616   0.00028165751
+      4600          96   0.0007048497   0.0007048497   0.00089917743  0.00018721659
+      4700          96   0.00070321437  0.00070321437  0.00093327157  0.00027581655
+      4800          96   0.00069636212  0.00069636212  0.00095998895  0.00026832587
+      4900          96   0.00066716522  0.00066716522  0.00098882541  0.00024920816
+      5000          96   0.00063786253  0.00063786253  0.00084144507  0.0006959824 
+Loop time of 12.6651 on 1 procs for 5000 steps with 96 atoms
+
+Performance: 170547.688 tau/day, 394.786 timesteps/s, 37.899 katom-step/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.13399    | 0.13399    | 0.13399    |   0.0 |  1.06
+Neigh   | 0.067145   | 0.067145   | 0.067145   |   0.0 |  0.53
+Comm    | 0.025541   | 0.025541   | 0.025541   |   0.0 |  0.20
+Output  | 10.654     | 10.654     | 10.654     |   0.0 | 84.12
+Modify  | 1.7142     | 1.7142     | 1.7142     |   0.0 | 13.53
+Other   |            | 0.06978    |            |       |  0.55
+
+Nlocal:             96 ave          96 max          96 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:            148 ave         148 max         148 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148
+Ave neighs/atom = 1.5416667
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.62 | 10.62 | 10.62 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000          96   0.00063786253  0.00063786253  0.00084144507  0.00068409102
+      5100          96   0.028313992    0.028313992    0.02867394     0.0064318866 
+      5200          94   0.039240682    0.039240682    0.046630048    0.0021250045 
+      5300          94   0.045894493    0.045894493    0.051041657    0.004288554  
+      5400          90   0.046049624    0.046049624    0.052748479    0.0023413632 
+      5500          89   0.044619749    0.044619749    0.051759567    0.0025268066 
+      5600          87   0.046502592    0.046502592    0.052805904    0.0022671331 
+      5700          86   0.047502773    0.047502773    0.052890192    0.0025018431 
+      5800          83   0.049317538    0.049317538    0.052470227    0.0024522166 
+      5900          81   0.051463883    0.051463883    0.053324316    0.0024303621 
+      6000          79   0.052996121    0.052996121    0.054122681    0.0024352971 
+      6100          78   0.048074683    0.048074683    0.051044879    0.0020985852 
+      6200          75   0.04840275     0.04840275     0.049998948    0.0020567512 
+      6300          74   0.048896993    0.048896993    0.05012768     0.0020235986 
+      6400          72   0.048661741    0.048661741    0.047914934    0.0027397448 
+      6500          72   0.049815101    0.049815101    0.04823434     0.0022998212 
+      6600          72   0.050578127    0.050578127    0.047972859    0.0023500543 
+      6700          71   0.053700957    0.053700957    0.049203548    0.0021231176 
+      6800          70   0.054955705    0.054955705    0.048252513    0.0022219662 
+      6900          69   0.055089911    0.055089911    0.048327243    0.0021431702 
+      7000          68   0.054713581    0.054713581    0.047461258    0.0027194558 
+      7100          68   0.055154516    0.055154516    0.048042367    0.0020996652 
+      7200          68   0.052688949    0.052688949    0.047223673    0.0031629618 
+      7300          66   0.053031698    0.053031698    0.046492962    0.0020164648 
+      7400          66   0.053814798    0.053814798    0.048105161    0.0019830573 
+      7500          64   0.050060478    0.050060478    0.046862322    0.0017880464 
+      7600          63   0.051383282    0.051383282    0.047500425    0.0018639548 
+      7700          61   0.047761405    0.047761405    0.045091014    0.001632776  
+      7800          60   0.047463305    0.047463305    0.045176189    0.001591933  
+      7900          60   0.048347642    0.048347642    0.046537806    0.0016308357 
+      8000          58   0.04714196     0.04714196     0.045527272    0.0015641403 
+      8100          58   0.046968881    0.046968881    0.04598277     0.0024094931 
+      8200          57   0.046997734    0.046997734    0.045676536    0.0014922033 
+      8300          57   0.045562254    0.045562254    0.045872476    0.0014466327 
+      8400          55   0.044408194    0.044408194    0.045223172    0.0013596468 
+      8500          55   0.043334554    0.043334554    0.045957536    0.0013267805 
+      8600          52   0.0407858      0.0407858      0.043378073    0.0011793941 
+      8700          52   0.039828276    0.039828276    0.043948609    0.0014514912 
+      8800          50   0.038530301    0.038530301    0.043112182    0.0010705032 
+      8900          50   0.038936121    0.038936121    0.044360368    0.0010817763 
+      9000          49   0.038340922    0.038340922    0.043586145    0.0010435081 
+      9100          48   0.037704467    0.037704467    0.043398687    0.0010047485 
+      9200          48   0.039439971    0.039439971    0.045446967    0.0010509895 
+      9300          48   0.040146494    0.040146494    0.047222767    0.0010698143 
+      9400          46   0.036196314    0.036196314    0.04514472     0.00092352701
+      9500          44   0.035428166    0.035428166    0.043156558    0.00086370075
+      9600          44   0.036236057    0.036236057    0.045015316    0.00088339425
+      9700          43   0.033612512    0.033612512    0.042808614    0.0008003869 
+      9800          42   0.034119077    0.034119077    0.043448026    0.0007931345 
+      9900          41   0.033534569    0.033534569    0.04281968     0.00076053851
+     10000          40   0.032867612    0.032867612    0.041673148    0.00072678237
+Loop time of 11.4047 on 1 procs for 5000 steps with 40 atoms
+
+Performance: 189395.206 tau/day, 438.415 timesteps/s, 17.537 katom-step/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0808     | 0.0808     | 0.0808     |   0.0 |  0.71
+Neigh   | 0.059506   | 0.059506   | 0.059506   |   0.0 |  0.52
+Comm    | 0.016313   | 0.016313   | 0.016313   |   0.0 |  0.14
+Output  | 9.7783     | 9.7783     | 9.7783     |   0.0 | 85.74
+Modify  | 1.4124     | 1.4124     | 1.4124     |   0.0 | 12.38
+Other   |            | 0.05743    |            |       |  0.50
+
+Nlocal:             40 ave          40 max          40 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:             18 ave          18 max          18 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18
+Ave neighs/atom = 0.45
+Neighbor list builds = 333
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.62 | 10.62 | 10.62 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          40   0.032867612    0.032867612    0.041673148    0.00072685327
+     10100          40   0.0076052221   0.0076052221   0.0076988542   0.00016814267
+     10200          40   0.0032668297   0.0032668297   0.0038743591   0.00054487661
+     10300          40   0.003316664    0.003316664    0.0040375473   7.3327605e-05
+     10400          40   0.0030064853   0.0030064853   0.0039975834   6.6469913e-05
+     10500          40   0.0030342866   0.0030342866   0.004203116    6.7084568e-05
+     10600          40   0.0030020199   0.0030020199   0.0043687727   6.6371188e-05
+     10700          40   0.0027999261   0.0027999261   0.003947504    0.00010754343
+     10800          40   0.0027031744   0.0027031744   0.0038359994   6.3984417e-05
+     10900          40   0.0027373574   0.0027373574   0.0039800535   7.0481083e-05
+     11000          39   0.0029362062   0.0029362062   0.002978473    6.9069963e-05
+     11100          39   0.0037840086   0.0037840086   0.0036639284   8.1514925e-05
+     11200          39   0.0045558771   0.0045558771   0.0041248127   9.8142478e-05
+     11300          39   0.0017981927   0.0017981927   0.0025146205   0.00031779839
+     11400          39   0.0016431107   0.0016431107   0.0024756094   4.4978596e-05
+     11500          39   0.0017504997   0.0017504997   0.0026753481   4.7200446e-05
+     11600          39   0.0020008726   0.0020008726   0.0029721732   5.2678933e-05
+     11700          39   0.0014870059   0.0014870059   0.0026506345   4.152681e-05 
+     11800          39   0.0016074438   0.0016074438   0.002888528   -3.0912602e-05
+     11900          39   0.0017722588   0.0017722588   0.0031282687   4.1702851e-05
+     12000          39   0.0027430864   0.0027430864   0.0039301824   6.8654618e-05
+     12100          39   0.0031883241   0.0031883241   0.0041806787   7.8260758e-05
+     12200          38   0.0013269284   0.0013269284   0.0032322246   3.6635105e-05
+     12300          38   0.0016569097   0.0016569097   0.0036433609   0.00041718571
+     12400          38   0.00094008147  0.00094008147  0.0033452514   3.7496272e-05
+     12500          37   0.00095698445  0.00095698445  0.0023073129   3.715434e-05 
+     12600          37   0.00098175769  0.00098175769  0.0025359749   3.7459507e-05
+     12700          37   0.0010099586   0.0010099586   0.0027775856   3.7772603e-05
+     12800          37   0.0010435337   0.0010435337   0.0030319623   3.811889e-05 
+     12900          37   0.0011032701   0.0011032701   0.0032983521   2.3599435e-05
+     13000          37   0.0012957624   0.0012957624   0.003683326    4.2333566e-05
+     13100          37   0.0010512853   0.0010512853   0.0037476793   3.6717097e-05
+     13200          37   0.0010868252   0.0010868252   0.0040740128   0.00018164133
+     13300          37   0.0011180293   0.0011180293   0.0044202397   3.643358e-05 
+     13400          37   0.0011178538   0.0011178538   0.0047516047   3.5746318e-05
+     13500          37   0.0007777481   0.0007777481   0.0037726389   5.3444345e-05
+     13600          36   0.0007999147   0.0007999147   0.003070242    3.248155e-05 
+     13700          36   0.0008389068   0.0008389068   0.003346172    2.9660005e-05
+     13800          36   0.00086583182  0.00086583182  0.0036410575   3.0212331e-05
+     13900          36   0.00058473604  0.00058473604  0.0024273755   5.7952251e-05
+     14000          36   0.00055727478  0.00055727478  0.0019113805   0.00011095694
+     14100          35   0.00044295291  0.00044295291  0.00066952242  0.00050643096
+     14200          35   0.00041514525  0.00041514525  0.00045222556  9.4438091e-05
+     14300          35   0.00042269774  0.00042269774  0.00047195914  4.5343892e-05
+     14400          35   0.00042495865  0.00042495865  0.00049753292  4.5106479e-05
+     14500          35   0.00040895208  0.00040895208  0.00051927404  4.6530808e-05
+     14600          35   0.00039129621  0.00039129621  0.00054194363  0.00019698404
+     14700          35   0.00039266334  0.00039266334  0.00058307961  4.7472072e-05
+     14800          35   0.00040570773  0.00040570773  0.00065710296  4.7982077e-05
+     14900          35   0.00040991932  0.00040991932  0.0007334058   4.8236973e-05
+     15000          35   0.00041469341  0.00041469341  0.00081836212  4.8450505e-05
+Loop time of 9.86119 on 1 procs for 5000 steps with 35 atoms
+
+Performance: 219040.411 tau/day, 507.038 timesteps/s, 17.746 katom-step/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.046258   | 0.046258   | 0.046258   |   0.0 |  0.47
+Neigh   | 0.0050304  | 0.0050304  | 0.0050304  |   0.0 |  0.05
+Comm    | 0.012996   | 0.012996   | 0.012996   |   0.0 |  0.13
+Output  | 8.9213     | 8.9213     | 8.9213     |   0.0 | 90.47
+Modify  | 0.82839    | 0.82839    | 0.82839    |   0.0 |  8.40
+Other   |            | 0.04723    |            |       |  0.48
+
+Nlocal:             35 ave          35 max          35 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:             26 ave          26 max          26 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 26
+Ave neighs/atom = 0.74285714
+Neighbor list builds = 37
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/gransurf/log.1Jul24.tri.gran.global.stl.g++.4

@@ -0,0 +1,316 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box	2 box   # simply for dump_modify to color lines = green
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  2 by 2 by 1 MPI processor grid
+
+pair_style	gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global surf.tri.stl hooke                 4000.0 NULL 100.0 NULL 0.5 1
+Reading STL object STL version of surf.tri from text file surf.tri.stl
+#fix             20 all surface/global surf.tri.stl hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins all pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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 = 22 22 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.786 | 5.786 | 5.786 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+       100          24   0.43156905     0.43156905     0.21119336     0.005627034  
+       200          24   0.73291569     0.73291569     0.35866087     0.009556157  
+       300          24   1.125323       1.125323       0.55068998     0.014672579  
+       400          24   1.608791       1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          44   1.0393538      1.0393538      0.51608705     0.025335722  
+       600          44   0.91758637     0.91758637     0.46172806     0.022367468  
+       700          44   0.94006427     0.94006427     0.48254195     0.035377091  
+       800          44   0.79393033     0.79393033     0.42561821     0.019944664  
+       900          68   0.72089876     0.72089876     0.37868178     0.027381075  
+      1000          68   0.63399342     0.63399342     0.33666552     0.052128303  
+      1100          68   0.63724402     0.63724402     0.3383098      0.024876228  
+      1200          68   0.61528554     0.61528554     0.33134629     0.030248652  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          88   0.45289831     0.45289831     0.24603739     0.032314185  
+      1400          88   0.51028258     0.51028258     0.27462447     0.027721293  
+      1500          88   0.52728648     0.52728648     0.28580371     0.030249652  
+      1600          88   0.46373765     0.46373765     0.25474076     0.023383063  
+      1700         100   0.32521568     0.32521568     0.18562847     0.044525945  
+      1800         100   0.30850324     0.30850324     0.17882757     0.031769348  
+      1900         100   0.25365045     0.25365045     0.15147723     0.020592523  
+      2000         100   0.21618068     0.21618068     0.12797228     0.016906764  
+      2100         100   0.24765668     0.24765668     0.13878326     0.014412505  
+      2200         100   0.23385636     0.23385636     0.13254109     0.028043759  
+      2300          99   0.11484144     0.11484144     0.07191588     0.013339992  
+      2400          99   0.053908946    0.053908946    0.042287303    0.0035096828 
+      2500          99   0.042127084    0.042127084    0.032805289    0.0034968494 
+      2600          98   0.03620012     0.03620012     0.027643861    0.0031757884 
+      2700          98   0.030497382    0.030497382    0.02276464     0.0062433907 
+      2800          98   0.025840421    0.025840421    0.019571636    0.0017100476 
+      2900          98   0.020282706    0.020282706    0.01512433     0.0039918866 
+      3000          97   0.011469683    0.011469683    0.0095129501   0.00083264863
+      3100          97   0.011061428    0.011061428    0.0089852941   0.0011413524 
+      3200          97   0.0085729018   0.0085729018   0.0065027781   0.0015793608 
+      3300          97   0.0048844117   0.0048844117   0.0043831348   0.00054654825
+      3400          97   0.0031718513   0.0031718513   0.002919676    0.00041030186
+      3500          97   0.0026149541   0.0026149541   0.0024273609   0.00064176505
+      3600          96   0.0022374762   0.0022374762   0.0021346878   0.0009000487 
+      3700          96   0.002015425    0.002015425    0.0019283015   0.00010102156
+      3800          96   0.0016640247   0.0016640247   0.0016542081   0.00058063795
+      3900          96   0.0014953491   0.0014953491   0.0015554014   0.00043366101
+      4000          96   0.0014314643   0.0014314643   0.001549993    0.00016144849
+      4100          96   0.0012797618   0.0012797618   0.001462077    0.0001478758 
+      4200          96   0.001301217    0.001301217    0.0015150334   0.00032745678
+      4300          96   0.0011719389   0.0011719389   0.0013301205   0.00025779628
+      4400          96   0.00092491728  0.00092491728  0.0010319633   0.00030044217
+      4500          96   0.00087292243  0.00087292243  0.001019192    0.00025577747
+      4600          96   0.00075144495  0.00075144495  0.00091990059  0.00018817234
+      4700          96   0.00074883306  0.00074883306  0.00093930259  0.0005619372 
+      4800          96   0.00065460832  0.00065460832  0.00089919023  0.00024621022
+      4900          96   0.0006499224   0.0006499224   0.00092528447  0.00026790153
+      5000          96   0.00061981936  0.00061981936  0.00078233948  0.00061552671
+Loop time of 15.3967 on 4 procs for 5000 steps with 96 atoms
+
+Performance: 140290.241 tau/day, 324.746 timesteps/s, 31.176 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.065219   | 0.068376   | 0.070577   |   0.8 |  0.44
+Neigh   | 0.036209   | 0.037389   | 0.038344   |   0.4 |  0.24
+Comm    | 0.94586    | 0.95361    | 0.96234    |   0.6 |  6.19
+Output  | 11.31      | 11.99      | 13.148     |  21.9 | 77.87
+Modify  | 0.7825     | 0.88835    | 0.95807    |   7.7 |  5.77
+Other   |            | 1.459      |            |       |  9.48
+
+Nlocal:             24 ave          25 max          22 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:           9.25 ave          12 max           8 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Neighs:          36.25 ave          40 max          34 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 145
+Ave neighs/atom = 1.5104167
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.6 | 10.6 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000          96   0.00061981936  0.00061981936  0.00078233948  0.00061520755
+      5100          96   0.028314129    0.028314129    0.028887614    0.0015596074 
+      5200          93   0.038280284    0.038280284    0.045433502    0.003972808  
+      5300          92   0.044602602    0.044602602    0.050026258    0.0066549492 
+      5400          88   0.043591861    0.043591861    0.050587055    0.0021499387 
+      5500          88   0.043643437    0.043643437    0.051930078    0.0045848219 
+      5600          86   0.044398335    0.044398335    0.050588091    0.0021861193 
+      5700          86   0.048834817    0.048834817    0.052122986    0.0024353201 
+      5800          82   0.048657023    0.048657023    0.050882437    0.0022637024 
+      5900          79   0.047422209    0.047422209    0.050391753    0.0020519953 
+      6000          78   0.047430795    0.047430795    0.050706223    0.0020757537 
+      6100          76   0.047766342    0.047766342    0.050881831    0.0020365653 
+      6200          74   0.048553742    0.048553742    0.049322747    0.0040124193 
+      6300          73   0.050329565    0.050329565    0.050219503    0.0021932369 
+      6400          71   0.049899479    0.049899479    0.047423384    0.0019659021 
+      6500          71   0.051053882    0.051053882    0.048643589    0.0020292656 
+      6600          71   0.051795185    0.051795185    0.04927532     0.0023715227 
+      6700          69   0.052264693    0.052264693    0.048643292    0.0020434717 
+      6800          69   0.052349883    0.052349883    0.049265236    0.0020181077 
+      6900          68   0.051428051    0.051428051    0.048628957    0.0019545319 
+      7000          67   0.050476407    0.050476407    0.048064128    0.0018923271 
+      7100          67   0.050313513    0.050313513    0.048219142    0.001884633  
+      7200          67   0.050521342    0.050521342    0.047963518    0.0021063865 
+      7300          66   0.049017518    0.049017518    0.047288558    0.0018972353 
+      7400          65   0.048690842    0.048690842    0.048162015    0.0017669135 
+      7500          64   0.048934259    0.048934259    0.047906689    0.0019361894 
+      7600          62   0.048293135    0.048293135    0.047386457    0.0023701331 
+      7700          61   0.050821617    0.050821617    0.048266806    0.0018564185 
+      7800          60   0.052493396    0.052493396    0.049727548    0.0017921461 
+      7900          59   0.053162734    0.053162734    0.050327775    0.0017510558 
+      8000          57   0.051249525    0.051249525    0.048540418    0.0028770132 
+      8100          57   0.05261519     0.05261519     0.049923888    0.0016707326 
+      8200          55   0.051727022    0.051727022    0.047928098    0.0014557055 
+      8300          55   0.050489803    0.050489803    0.048163815    0.0033275674 
+      8400          54   0.049599363    0.049599363    0.047431898    0.0015088762 
+      8500          54   0.052050538    0.052050538    0.048908289    0.0015666966 
+      8600          52   0.050340482    0.050340482    0.046440415    0.0014555948 
+      8700          52   0.052028316    0.052028316    0.048176195    0.0015106353 
+      8800          50   0.0499901      0.0499901      0.045788044    0.0025087962 
+      8900          50   0.051750338    0.051750338    0.047753896    0.0014377545 
+      9000          50   0.051966831    0.051966831    0.048823952    0.0014437681 
+      9100          49   0.051660945    0.051660945    0.048110255    0.0014336784 
+      9200          49   0.051126513    0.051126513    0.048962201    0.0014162724 
+      9300          48   0.049057888    0.049057888    0.0492291      0.0013197818 
+      9400          48   0.045030047    0.045030047    0.047529619    0.0013481748 
+      9500          48   0.045513589    0.045513589    0.048536638    0.0012236674 
+      9600          48   0.043665627    0.043665627    0.048296609    0.0011806622 
+      9700          48   0.044106239    0.044106239    0.049540196    0.0011963288 
+      9800          46   0.042160287    0.042160287    0.048481885    0.0011107764 
+      9900          46   0.041772009    0.041772009    0.049483596    0.0011344326 
+     10000          44   0.040236277    0.040236277    0.045816406    0.00099962018
+Loop time of 14.3219 on 4 procs for 5000 steps with 44 atoms
+
+Performance: 150817.741 tau/day, 349.115 timesteps/s, 15.361 katom-step/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.045346   | 0.049249   | 0.05101    |   1.0 |  0.34
+Neigh   | 0.027653   | 0.028827   | 0.029969   |   0.5 |  0.20
+Comm    | 0.68027    | 0.70592    | 0.72986    |   2.2 |  4.93
+Output  | 10.707     | 11.401     | 12.544     |  22.1 | 79.61
+Modify  | 0.60999    | 0.65113    | 0.70846    |   4.7 |  4.55
+Other   |            | 1.485      |            |       | 10.37
+
+Nlocal:             11 ave          20 max           4 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Nghost:              4 ave           6 max           2 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:           9.75 ave          23 max           2 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 39
+Ave neighs/atom = 0.88636364
+Neighbor list builds = 333
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.6 | 10.6 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          44   0.040236277    0.040236277    0.045816406    0.00099979881
+     10100          44   0.010977052    0.010977052    0.010149182    0.00026758119
+     10200          44   0.004605352    0.004605352    0.0053045614   0.00011226198
+     10300          44   0.0053942032   0.0053942032   0.0056431085   0.00013149135
+     10400          44   0.0036859511   0.0036859511   0.0041662707   9.2662763e-05
+     10500          44   0.0039184347   0.0039184347   0.0043067155   0.00049979829
+     10600          44   0.0044427233   0.0044427233   0.0045879783   0.00011077625
+     10700          44   0.0029607594   0.0029607594   0.0034776101   0.0006068726 
+     10800          44   0.0026942916   0.0026942916   0.0034401136   6.706354e-05 
+     10900          44   0.0026203469   0.0026203469   0.0034492724   6.9607138e-05
+     11000          44   0.0019864947   0.0019864947   0.0031427116   8.3134017e-06
+     11100          44   0.0019240976   0.0019240976   0.0032808084   2.0347364e-05
+     11200          44   0.0018635948   0.0018635948   0.0034030363   5.7875998e-05
+     11300          44   0.0017686207   0.0017686207   0.0029556669   9.3363224e-05
+     11400          44   0.0014303652   0.0014303652   0.002751691    5.9528496e-05
+     11500          44   0.001399414    0.001399414    0.0027540021   5.8871141e-05
+     11600          44   0.0011285459   0.0011285459   0.0017454672   0.00063103388
+     11700          44   0.0010672518   0.0010672518   0.0014970714   0.00012978783
+     11800          44   0.0010754046   0.0010754046   0.0015525936   0.00011139988
+     11900          44   0.00093155287  0.00093155287  0.0011682302   0.00012515367
+     12000          44   0.00084853622  0.00084853622  0.0010681768   0.00010639935
+     12100          44   0.00069411148  0.00069411148  0.00077780972  7.3742549e-05
+     12200          44   0.0006859885   0.0006859885   0.0007696296   9.3309816e-05
+     12300          44   0.00064103944  0.00064103944  0.00072985388  0.0001474211 
+     12400          44   0.00063849822  0.00063849822  0.00072417306  9.4166534e-05
+     12500          44   0.0006361049   0.0006361049   0.00068646857  9.5282342e-05
+     12600          44   0.00063622199  0.00063622199  0.00068538208  9.5058162e-05
+     12700          44   0.00062165913  0.00062165913  0.00066876644  9.412044e-05 
+     12800          44   0.00058480739  0.00058480739  0.00063172101  0.00018653887
+     12900          44   0.00054058957  0.00054058957  0.00059549487  9.384774e-05 
+     13000          44   0.00051904254  0.00051904254  0.00057073513  9.4434337e-05
+     13100          44   0.00053410816  0.00053410816  0.00057766113  9.61856e-05  
+     13200          44   0.00050156547  0.00050156547  0.00055212122  9.7382505e-05
+     13300          44   0.00049740896  0.00049740896  0.00054826803  9.7690479e-05
+     13400          44   0.00049775099  0.00049775099  0.00054791017  9.7482658e-05
+     13500          44   0.00049205909  0.00049205909  0.00054071132  0.00010353798
+     13600          44   0.00049240333  0.00049240333  0.00054031425  9.7448102e-05
+     13700          44   0.00049274845  0.00049274845  0.00053984708  9.7497469e-05
+     13800          43   0.00050763917  0.00050763917  0.00055870605  8.5113661e-05
+     13900          43   0.00047304434  0.00047304434  0.00054545171  7.7477263e-05
+     14000          43   0.00047307851  0.00047307851  0.00056349029  0.00016615605
+     14100          43   0.00048268391  0.00048268391  0.00059292333  8.4939642e-05
+     14200          43   0.00049712412  0.00049712412  0.00064043909  8.522618e-05 
+     14300          43   0.00051010248  0.00051010248  0.00069557642  8.5161341e-05
+     14400          43   0.0005010299   0.0005010299   0.00074528156  8.5292218e-05
+     14500          43   0.00050900735  0.00050900735  0.00081321917  8.5452422e-05
+     14600          43   0.00051293789  0.00051293789  0.00088464504  8.5523903e-05
+     14700          43   0.00050022161  0.00050022161  0.00094898195  8.520624e-05 
+     14800          43   0.00049641051  0.00049641051  0.0010219267   8.5106195e-05
+     14900          43   0.00048906772  0.00048906772  0.0010926634   8.4926556e-05
+     15000          43   0.00048008443  0.00048008443  0.0011603655   8.470585e-05 
+Loop time of 14.5369 on 4 procs for 5000 steps with 43 atoms
+
+Performance: 148587.184 tau/day, 343.952 timesteps/s, 14.790 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.020082   | 0.038623   | 0.055378   |   6.7 |  0.27
+Neigh   | 0.00203    | 0.0025526  | 0.0032587  |   0.9 |  0.02
+Comm    | 0.46528    | 0.54133    | 0.62211    |   7.5 |  3.72
+Output  | 10.574     | 11.671     | 12.961     |  26.2 | 80.28
+Modify  | 0.20883    | 0.41514    | 0.69875    |  27.7 |  2.86
+Other   |            | 1.869      |            |       | 12.85
+
+Nlocal:          10.75 ave          20 max           5 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:              4 ave           7 max           2 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:             10 ave          22 max           2 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 40
+Ave neighs/atom = 0.93023256
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:00:46

examples/gransurf/log.1Jul24.tri.gran.surf.g++.1

@@ -0,0 +1,345 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  1 by 1 by 1 MPI processor grid
+
+molecule        tris surf.tri
+Read molecule template tris:
+LAMMPS data file for tri plane
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  4 triangles
+fix             20 all surface/local tris
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.33 | 13.33 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95089817     1.0393538      0.51608705     0.025335722  
+       600          48   0.83949391     0.91758637     0.46172806     0.022515854  
+       700          48   0.8600588      0.94006427     0.48254195     0.046349308  
+       800          48   0.72636179     0.79393033     0.42561821     0.02213745   
+       900          72   0.68028474     0.72089876     0.37868178     0.028124504  
+      1000          72   0.59827548     0.63399342     0.33666552     0.057932603  
+      1100          72   0.60134295     0.63724402     0.3383098      0.025565346  
+      1200          72   0.58062156     0.61528554     0.33134629     0.031222266  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.43299069     0.45289831     0.24603739     0.033378543  
+      1400          92   0.48785257     0.51028258     0.27462447     0.029606478  
+      1500          92   0.50410905     0.52728648     0.28580371     0.031570548  
+      1600          92   0.44335358     0.46373765     0.25474076     0.025856762  
+      1700         104   0.31258594     0.32521568     0.18562847     0.056917788  
+      1800         104   0.29652255     0.30850326     0.17882758     0.036853847  
+      1900         104   0.2438002      0.25365071     0.15147734     0.027067985  
+      2000         104   0.20778515     0.21618051     0.12797216     0.024491014  
+      2100         104   0.23803938     0.24765713     0.13878356     0.018557519  
+      2200         104   0.22477903     0.23386101     0.13254455     0.034204374  
+      2300         103   0.11028018     0.11478141     0.071880248    0.023107934  
+      2400         103   0.051939416    0.054059392    0.04238437     0.010076125  
+      2500         103   0.04046389     0.042115477    0.03276739     0.0092675482 
+      2600         102   0.034504146    0.035926998    0.027152703    0.012043982  
+      2700         102   0.029660748    0.030883871    0.023043461    0.0098675596 
+      2800         102   0.023675472    0.02465178     0.018814934    0.0079223517 
+      2900         102   0.01955555     0.020361964    0.015095009    0.010178019  
+      3000         101   0.010976926    0.011434298    0.0094599476   0.0062989926 
+      3100         101   0.010404873    0.01083841     0.0088413578   0.006904568  
+      3200         101   0.0084790802   0.0088323752   0.0067474787   0.0078181584 
+      3300         101   0.0049651339   0.0051720145   0.0045655092   0.0077852556 
+      3400         101   0.0028770081   0.0029968834   0.0028180577   0.0065531061 
+      3500         101   0.0026603851   0.0027712345   0.0026301508   0.0066265532 
+      3600         100   0.0022879435   0.002384278    0.0022868891   0.005946377  
+      3700         100   0.0020797371   0.002167305    0.0021366338   0.0060275426 
+      3800         100   0.0018223254   0.0018990549   0.0018542925   0.0058665012 
+      3900         100   0.0016056933   0.0016733014   0.0017380009   0.0065755667 
+      4000         100   0.0012764017   0.001330145    0.0014831053   0.0057002441 
+      4100         100   0.0011732772   0.0012226783   0.0014520833   0.0058997102 
+      4200         100   0.0011509224   0.0011993823   0.0014499925   0.005891705  
+      4300         100   0.00093450709  0.00097385475  0.0011305405   0.0060755638 
+      4400         100   0.00073710728  0.00076814338  0.00093491029  0.005994252  
+      4500         100   0.00066950467  0.00069769434  0.00081329183  0.0060209889 
+      4600         100   0.00067057619  0.00069881097  0.00081870364  0.0066002598 
+      4700         100   0.00061522957  0.00064113397  0.0007867969   0.0061000762 
+      4800         100   0.00057127674  0.0005953305   0.00078435449  0.006075934  
+      4900         100   0.00048538112  0.00050581822  0.00067082262  0.0061360807 
+      5000         100   0.00049531306  0.00051616835  0.00070658811  0.0061425578 
+Loop time of 0.232999 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 9270416.385 tau/day, 21459.297 timesteps/s, 2.146 Matom-step/s
+96.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.025378   | 0.025378   | 0.025378   |   0.0 | 10.89
+Neigh   | 0.0083862  | 0.0083862  | 0.0083862  |   0.0 |  3.60
+Comm    | 0.00040258 | 0.00040258 | 0.00040258 |   0.0 |  0.17
+Output  | 0.18672    | 0.18672    | 0.18672    |   0.0 | 80.14
+Modify  | 0.011026   | 0.011026   | 0.011026   |   0.0 |  4.73
+Other   |            | 0.001084   |            |       |  0.47
+
+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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 320
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.46 | 14.46 | 14.46 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00049531306  0.00051616835  0.00070658811  0.0061401156 
+      5100         100   0.51797813     0.029144789    0.028561434    0.061796302  
+      5200          99   0.53766867     0.044472871    0.048736594    0.052595853  
+      5300          98   0.54821886     0.050173651    0.052878851    0.060444985  
+      5400          95   0.56483365     0.050925371    0.053737351    0.057837587  
+      5500          95   0.56809688     0.054333638    0.055612067    0.043728998  
+      5600          92   0.58741732     0.056826396    0.056374971    0.039138605  
+      5700          92   0.59268005     0.062331088    0.059265481    0.035680319  
+      5800          88   0.62103092     0.066489286    0.060222709    0.035282967  
+      5900          88   0.62345455     0.069029715    0.0628021      0.035017077  
+      6000          85   0.64509294     0.070959095    0.06202824     0.035049999  
+      6100          84   0.65441054     0.07348095     0.062757785    0.035609875  
+      6200          81   0.67575597     0.07301839     0.059946946    0.034382094  
+      6300          80   0.68384452     0.073501833    0.059856228    0.03514656   
+      6400          78   0.7013697      0.075265575    0.059538181    0.034094416  
+      6500          78   0.70386686     0.077899568    0.06122273     0.034195388  
+      6600          77   0.7136876      0.079571915    0.062523938    0.034262144  
+      6700          75   0.73326389     0.082149266    0.061775684    0.036880856  
+      6800          74   0.74125199     0.081163997    0.060577178    0.034065559  
+      6900          73   0.74794382     0.078542284    0.058822059    0.034265565  
+      7000          72   0.75869051     0.0799395      0.060173988    0.03372964   
+      7100          71   0.76478565     0.076119935    0.058622864    0.033529799  
+      7200          70   0.77534407     0.076733249    0.059389913    0.033359627  
+      7300          69   0.78737597     0.078601354    0.060601057    0.03387736   
+      7400          68   0.79334599     0.073700033    0.058720823    0.033449993  
+      7500          65   0.82643666     0.07301444     0.057725758    0.033058102  
+      7600          64   0.83647393     0.070962335    0.057196688    0.034325146  
+      7700          64   0.83136046     0.065502199    0.054505995    0.033284476  
+      7800          63   0.84413416     0.065952385    0.055713645    0.032527019  
+      7900          63   0.84474799     0.066608547    0.057188344    0.032380197  
+      8000          63   0.84601678     0.067964843    0.059162055    0.035623321  
+      8100          62   0.85442995     0.063318376    0.056917075    0.033794671  
+      8200          60   0.87886485     0.060762667    0.053902381    0.031778389  
+      8300          60   0.88023598     0.062233516    0.05567968     0.032190408  
+      8400          58   0.91091634     0.064361351    0.056842653    0.031999455  
+      8500          58   0.91076207     0.064195441    0.056598399    0.031981767  
+      8600          57   0.92732215     0.065749251    0.058085176    0.031964139  
+      8700          56   0.94060812     0.063183664    0.057132444    0.031795486  
+      8800          54   0.97102642     0.060271847    0.054931651    0.031534156  
+      8900          53   0.98835079     0.06006587     0.054799498    0.031664682  
+      9000          52   1.0052014      0.058599798    0.0548155      0.031347041  
+      9100          51   1.0232141      0.057600571    0.054358272    0.031293028  
+      9200          51   1.0234203      0.057824665    0.055491376    0.031272133  
+      9300          50   1.0422387      0.056858101    0.055336743    0.031184651  
+      9400          49   1.0607968      0.054708372    0.054237694    0.031018741  
+      9500          49   1.0598447      0.053669652    0.05412067     0.030987958  
+      9600          47   1.0997672      0.049481209    0.049207618    0.030830628  
+      9700          47   1.1009351      0.050760379    0.05160771     0.030681632  
+      9800          46   1.1225281      0.048846024    0.052582727    0.030659518  
+      9900          46   1.1235541      0.049972117    0.054322137    0.030823675  
+     10000          43   1.1964897      0.045828636    0.049253726    0.03048984   
+Loop time of 0.211297 on 1 procs for 5000 steps with 43 atoms
+
+Performance: 10222583.456 tau/day, 23663.388 timesteps/s, 1.018 Matom-step/s
+96.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.021317   | 0.021317   | 0.021317   |   0.0 | 10.09
+Neigh   | 0.0047466  | 0.0047466  | 0.0047466  |   0.0 |  2.25
+Comm    | 0.00037942 | 0.00037942 | 0.00037942 |   0.0 |  0.18
+Output  | 0.1732     | 0.1732     | 0.1732     |   0.0 | 81.97
+Modify  | 0.010709   | 0.010709   | 0.010709   |   0.0 |  5.07
+Other   |            | 0.0009465  |            |       |  0.45
+
+Nlocal:             43 ave          43 max          43 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 208
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  39 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.58 | 13.58 | 13.58 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          43   0.041464004    0.045828636    0.049253726    0.002992911  
+     10100          43   0.01536718     0.016984778    0.018346335    0.0026107883 
+     10200          43   0.013276935    0.014674507    0.018130285    0.0032805934 
+     10300          43   0.012643213    0.013974077    0.019027228    0.0020933246 
+     10400          43   0.012779466    0.014124673    0.019370488    0.0026402198 
+     10500          43   0.012399341    0.013704535    0.019539407    0.0022259887 
+     10600          43   0.012201003    0.013485319    0.018098349    0.0024634333 
+     10700          43   0.012655256    0.013987388    0.019496323    0.002221395  
+     10800          43   0.012579162    0.013903285    0.019865363    0.0032621089 
+     10900          43   0.012810408    0.014158872    0.020704867    0.0024564532 
+     11000          43   0.013492114    0.014912337    0.020426966    0.0021076994 
+     11100          43   0.012081727    0.013353488    0.019941305    0.0027605259 
+     11200          43   0.011157364    0.012331823    0.019789593    0.0022805894 
+     11300          43   0.011311656    0.012502357    0.020672585    0.0045512862 
+     11400          43   0.010835381    0.011975948    0.019984802    0.002500184  
+     11500          43   0.010883617    0.012029261    0.020161482    0.0024288947 
+     11600          43   0.010601773    0.011717749    0.02043478     0.002518671  
+     11700          43   0.010652376    0.011773679    0.020877142    0.0047191948 
+     11800          43   0.010586149    0.01170048     0.021045412    0.0029958449 
+     11900          42   0.010310675    0.011425342    0.020890641    0.0041299678 
+     12000          42   0.0096193697   0.010659302    0.01734171     0.0055638559 
+     12100          42   0.0090012199   0.0099743248   0.015925878    0.0062568296 
+     12200          42   0.0092694202   0.01027152     0.016223404    0.0031650129 
+     12300          41   0.009275497    0.010306108    0.016491126    0.0051047425 
+     12400          40   0.010347045    0.011529564    0.01780755     0.0020187837 
+     12500          40   0.010872959    0.012115582    0.018095787    0.0017574207 
+     12600          39   0.0094147621   0.010522381    0.018210318    0.0017051826 
+     12700          39   0.0086581705   0.0096767788   0.018566587    0.0018394808 
+     12800          39   0.0082190204   0.009185964    0.018898421    0.003442822  
+     12900          39   0.0078768039   0.0088034867   0.019645193    0.0024525382 
+     13000          39   0.0066934943   0.0074809642   0.016840831    0.0042565543 
+     13100          38   0.0063530854   0.0071231563   0.015836167    0.0033482203 
+     13200          38   0.0067586397   0.0075778688   0.016370483    0.0027718974 
+     13300          37   0.0062831006   0.0070684882   0.016770756    0.0028166814 
+     13400          36   0.005492839    0.0062015924   0.01655756     0.0041562248 
+     13500          36   0.0052681628   0.0059479258   0.011983298    0.0035740396 
+     13600          36   0.0053786817   0.0060727051   0.011670978    0.004098456  
+     13700          36   0.0055059193   0.0062163605   0.01170773     0.0023640523 
+     13800          35   0.0055296574   0.0062669451   0.0119576      0.0031972222 
+     13900          34   0.0052354859   0.0059576219   0.012092776    0.0016695231 
+     14000          33   0.0050682191   0.0057922504   0.01250025     0.0015032079 
+     14100          33   0.0051315263   0.0058646015   0.01289725     0.0014073536 
+     14200          33   0.005254278    0.0060048892   0.012894635    0.0014096146 
+     14300          33   0.0057832225   0.0066093971   0.013867573    0.001419376  
+     14400          33   0.0058060441   0.006635479    0.014475826    0.0025855623 
+     14500          33   0.0058141643   0.0066447593   0.015171174    0.0024244841 
+     14600          32   0.0055995745   0.0064291411   0.016022968    0.0014230432 
+     14700          32   0.0055988198   0.0064282746   0.016907696    0.0015101902 
+     14800          32   0.0057678876   0.0066223895   0.017482798    0.0016956915 
+     14900          32   0.0057096482   0.006555522    0.018478553    0.0019276435 
+     15000          32   0.0057085079   0.0065542128   0.017574244    0.0021196367 
+Loop time of 0.172151 on 1 procs for 5000 steps with 32 atoms
+
+Performance: 12547152.387 tau/day, 29044.334 timesteps/s, 929.419 katom-step/s
+90.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.010881   | 0.010881   | 0.010881   |   0.0 |  6.32
+Neigh   | 0.00081386 | 0.00081386 | 0.00081386 |   0.0 |  0.47
+Comm    | 0.00028458 | 0.00028458 | 0.00028458 |   0.0 |  0.17
+Output  | 0.15425    | 0.15425    | 0.15425    |   0.0 | 89.60
+Modify  | 0.0052213  | 0.0052213  | 0.0052213  |   0.0 |  3.03
+Other   |            | 0.0006992  |            |       |  0.41
+
+Nlocal:             32 ave          32 max          32 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 73
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.surf.g++.4

@@ -0,0 +1,346 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  2 by 2 by 1 MPI processor grid
+
+molecule        tris surf.tri
+Read molecule template tris:
+LAMMPS data file for tri plane
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  4 triangles
+fix             20 all surface/local tris
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.47 | 12.69 | 13.35 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95089817     1.0393538      0.51608705     0.025335722  
+       600          48   0.83949391     0.91758637     0.46172806     0.022515854  
+       700          48   0.8600588      0.94006427     0.48254195     0.046349308  
+       800          48   0.72636179     0.79393033     0.42561821     0.02213745   
+       900          72   0.68028474     0.72089876     0.37868178     0.028124504  
+      1000          72   0.59827548     0.63399342     0.33666552     0.057932603  
+      1100          72   0.60134295     0.63724402     0.3383098      0.025565346  
+      1200          72   0.58062156     0.61528554     0.33134629     0.031222266  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.43299069     0.45289831     0.24603739     0.033378543  
+      1400          92   0.48785257     0.51028258     0.27462447     0.029606478  
+      1500          92   0.50410905     0.52728648     0.28580371     0.031570548  
+      1600          92   0.44335358     0.46373765     0.25474076     0.025856762  
+      1700         104   0.31258594     0.32521568     0.18562847     0.056917788  
+      1800         104   0.29652255     0.30850326     0.17882758     0.036853847  
+      1900         104   0.2438002      0.25365071     0.15147734     0.027067985  
+      2000         104   0.20778515     0.21618051     0.12797216     0.024491012  
+      2100         104   0.23803938     0.24765713     0.13878356     0.018557518  
+      2200         104   0.22477903     0.23386101     0.13254455     0.034204387  
+      2300         103   0.11028018     0.11478141     0.071880246    0.023108123  
+      2400         103   0.051939196    0.054059163    0.042383035    0.0100614    
+      2500         103   0.040442247    0.042092951    0.032749381    0.01046781   
+      2600         102   0.034504426    0.035927289    0.027149368    0.012010718  
+      2700         102   0.029679791    0.0309037      0.023036586    0.010355503  
+      2800         102   0.023702803    0.024680238    0.018826345    0.007910395  
+      2900         102   0.019561868    0.020368542    0.015101556    0.010178779  
+      3000         101   0.010990893    0.011448847    0.0094754992   0.0063202976 
+      3100         101   0.010529472    0.0109682      0.0089009784   0.007388411  
+      3200         101   0.0084987177   0.0088528309   0.0067377904   0.0075443377 
+      3300         101   0.004926689    0.0051319677   0.0045207553   0.0078470774 
+      3400         101   0.0028833468   0.0030034862   0.0028132775   0.007922942  
+      3500         101   0.0026928316   0.0028050329   0.0026351323   0.0069014836 
+      3600         100   0.0022956296   0.0023922877   0.0022701552   0.0059851937 
+      3700         100   0.0021025959   0.0021911262   0.0021280497   0.0060105187 
+      3800         100   0.0018494532   0.0019273249   0.0018855471   0.0061456458 
+      3900         100   0.0016137385   0.0016816854   0.0017223036   0.0066454899 
+      4000         100   0.0013124128   0.0013676723   0.0014840612   0.0062470481 
+      4100         100   0.0012105075   0.0012614763   0.0014645791   0.0057688838 
+      4200         100   0.0011433138   0.0011914533   0.0014435934   0.0059579374 
+      4300         100   0.00098204031  0.0010233894   0.0012522874   0.0059816181 
+      4400         100   0.00076296239  0.00079508712  0.0009721438   0.0060246257 
+      4500         100   0.00066335366  0.00069128434  0.00091049427  0.006214887  
+      4600         100   0.00062039452  0.0006465164   0.00082139977  0.0060745906 
+      4700         100   0.00062069669  0.00064683129  0.00083492397  0.0064522652 
+      4800         100   0.00050639953  0.00052772161  0.00074517777  0.0062114309 
+      4900         100   0.00048181752  0.00050210458  0.00072773699  0.0061746147 
+      5000         100   0.00045281738  0.00047188337  0.00072834743  0.0067103321 
+Loop time of 0.313085 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 6899081.431 tau/day, 15970.096 timesteps/s, 1.597 Matom-step/s
+91.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0085396  | 0.008862   | 0.0089969  |   0.2 |  2.83
+Neigh   | 0.0031142  | 0.0032591  | 0.0034769  |   0.3 |  1.04
+Comm    | 0.050942   | 0.051859   | 0.053093   |   0.3 | 16.56
+Output  | 0.1382     | 0.17924    | 0.23814    |   9.2 | 57.25
+Modify  | 0.0066482  | 0.011589   | 0.015218   |   3.2 |  3.70
+Other   |            | 0.05827    |            |       | 18.61
+
+Nlocal:             25 ave          27 max          23 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:             75 ave          77 max          73 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00045281738  0.00047188337  0.00072834743  0.0066020848 
+      5100         100   0.51860744     0.029800601    0.029304106    0.051905706  
+      5200          98   0.53862917     0.040171507    0.047791716    0.050757979  
+      5300          96   0.55112647     0.042263021    0.050195999    0.04601151   
+      5400          93   0.56728592     0.04180938     0.050815028    0.037450075  
+      5500          93   0.56916149     0.043770195    0.053081459    0.03605744   
+      5600          91   0.58284551     0.045872284    0.05148537     0.033849288  
+      5700          90   0.59267876     0.049850941    0.05375731     0.035005112  
+      5800          86   0.61680698     0.04836437     0.052582503    0.033850751  
+      5900          85   0.62574796     0.050646859    0.054238313    0.034443643  
+      6000          82   0.64727841     0.050889245    0.052494508    0.033866734  
+      6100          80   0.66364069     0.052220462    0.052387252    0.033487505  
+      6200          78   0.67959846     0.052301399    0.050336285    0.033168524  
+      6300          78   0.6815537      0.054363773    0.051168788    0.033400067  
+      6400          76   0.69757373     0.053619014    0.048730817    0.033079249  
+      6500          76   0.69960717     0.055767015    0.050448147    0.034190142  
+      6600          75   0.71046572     0.05804834     0.050353278    0.033120738  
+      6700          73   0.73004213     0.059587557    0.050356776    0.033203715  
+      6800          72   0.73955244     0.059658858    0.049165521    0.033090601  
+      6900          72   0.73984252     0.05996626     0.04893239     0.03538438   
+      7000          72   0.73855905     0.05860616     0.048218057    0.032977368  
+      7100          71   0.74996747     0.060403683    0.049738231    0.032942299  
+      7200          71   0.74958163     0.059994462    0.04984795     0.034576756  
+      7300          71   0.74958014     0.059992886    0.050595934    0.033560699  
+      7400          69   0.77040618     0.060570951    0.05074398     0.032817955  
+      7500          68   0.78190055     0.061527899    0.051576944    0.032829232  
+      7600          67   0.79252938     0.061223545    0.051664985    0.033139179  
+      7700          67   0.79257577     0.061272925    0.052020235    0.032808213  
+      7800          67   0.79235064     0.06103327     0.052983733    0.032695163  
+      7900          65   0.81235659     0.057995702    0.051797211    0.032371751  
+      8000          65   0.81047528     0.05598897     0.051741533    0.032279411  
+      8100          63   0.83302221     0.054074089    0.049909885    0.03200106   
+      8200          62   0.84514204     0.053378682    0.050396436    0.032363269  
+      8300          61   0.85723702     0.052198956    0.049950193    0.031878528  
+      8400          60   0.86997524     0.051226536    0.050780002    0.031636653  
+      8500          60   0.86954615     0.050766237    0.051169838    0.036559517  
+      8600          58   0.89936909     0.051942618    0.050191748    0.037496085  
+      8700          58   0.89897047     0.05151391     0.051173535    0.034671574  
+      8800          56   0.93013263     0.051886568    0.052056826    0.031441238  
+      8900          55   0.94599772     0.051455942    0.052973742    0.034207698  
+      9000          53   0.97967117     0.050662944    0.052877672    0.035867184  
+      9100          51   1.0142291      0.047834254    0.050461469    0.032649796  
+      9200          50   1.033876       0.047752147    0.050703363    0.030822387  
+      9300          49   1.0547579      0.04812047     0.050590947    0.030893945  
+      9400          49   1.0558051      0.049262873    0.052436796    0.030873639  
+      9500          48   1.0767984      0.048801088    0.051653283    0.030786358  
+      9600          46   1.1213506      0.047553612    0.049643046    0.030642108  
+      9700          46   1.1227493      0.049088768    0.051778335    0.030603423  
+      9800          45   1.1452146      0.046959031    0.051250902    0.032613968  
+      9900          45   1.1460384      0.047865295    0.05426893     0.036176412  
+     10000          44   1.1711564      0.047401187    0.054529055    0.033327294  
+Loop time of 0.308457 on 4 procs for 5000 steps with 44 atoms
+
+Performance: 7002603.045 tau/day, 16209.729 timesteps/s, 713.228 katom-step/s
+92.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0076273  | 0.0083433  | 0.0095898  |   0.8 |  2.70
+Neigh   | 0.0016764  | 0.0017433  | 0.0018123  |   0.1 |  0.57
+Comm    | 0.041654   | 0.043513   | 0.044442   |   0.5 | 14.11
+Output  | 0.13868    | 0.18445    | 0.24355    |   9.3 | 59.80
+Modify  | 0.0052129  | 0.0055373  | 0.0062783  |   0.6 |  1.80
+Other   |            | 0.06487    |            |       | 21.03
+
+Nlocal:             11 ave          14 max           9 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:             33 ave          35 max          30 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 181
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  40 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.71 | 13.71 | 13.72 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          44   0.042991774    0.047401187    0.054529055    0.005835563  
+     10100          44   0.017515048    0.019311463    0.022242125    0.0054597963 
+     10200          44   0.016651387    0.018359221    0.021768919    0.007426361  
+     10300          43   0.016651808    0.01840463     0.019841598    0.0053906984 
+     10400          43   0.014274557    0.015777142    0.019217385    0.0055709619 
+     10500          43   0.013716602    0.015160455    0.019335926    0.005533805  
+     10600          43   0.012929871    0.01429091     0.019961256    0.0055113819 
+     10700          43   0.013249241    0.014643898    0.020488568    0.0057553732 
+     10800          43   0.010645141    0.011765682    0.020018164    0.0070545501 
+     10900          43   0.010177915    0.011249275    0.019638619    0.0090787871 
+     11000          43   0.010174433    0.011245426    0.019566189    0.0093512809 
+     11100          43   0.011130765    0.012302425    0.020051358    0.0093282449 
+     11200          42   0.011178858    0.012387383    0.020957174    0.0087638823 
+     11300          42   0.011335071    0.012560484    0.019605652    0.0085884944 
+     11400          42   0.00892055     0.0098849338   0.017254178    0.0115493    
+     11500          42   0.0087305707   0.0096744162   0.016920618    0.0072562207 
+     11600          42   0.0085763835   0.0095035601   0.016735424    0.0073524491 
+     11700          42   0.0091445266   0.010133124    0.016871267    0.0053996766 
+     11800          41   0.0079999518   0.0088888353   0.016813209    0.0052166459 
+     11900          41   0.0079421236   0.0088245818   0.01747319     0.0051109817 
+     12000          41   0.0075832184   0.0084257982   0.016889505    0.0064088798 
+     12100          40   0.0080007752   0.0089151496   0.017619052    0.005204876  
+     12200          40   0.0084961277   0.0094671138   0.0182733      0.007442812  
+     12300          40   0.0098721644   0.011000412    0.019497465    0.0058554546 
+     12400          39   0.0073872276   0.0082563132   0.017957824    0.0074206067 
+     12500          39   0.0074959064   0.0083777777   0.018236089    0.0083410154 
+     12600          39   0.0079646034   0.0089016156   0.018386853    0.010366406  
+     12700          38   0.007907691    0.008866199    0.013301549    0.002231989  
+     12800          37   0.0076214799   0.0085741649   0.013938502    0.0020598491 
+     12900          36   0.00691836     0.0078110516   0.013261785    0.0019344109 
+     13000          36   0.0063774393   0.0072003347   0.011546252    0.0021781987 
+     13100          35   0.0065688938   0.0074447463   0.011179758    0.0018476982 
+     13200          35   0.006608481    0.0074896118   0.011296542    0.0028753707 
+     13300          35   0.0070429905   0.007982056    0.011580455    0.0017137712 
+     13400          35   0.0069974233   0.007930413    0.011637164    0.0017013866 
+     13500          35   0.0070448152   0.0079841239   0.012227322    0.0016768457 
+     13600          35   0.0070302138   0.0079675757   0.012851645    0.0016524347 
+     13700          35   0.0070610122   0.0080024805   0.013351059    0.0016599408 
+     13800          35   0.0068527095   0.0077664041   0.013322016    0.0021396807 
+     13900          35   0.0068663277   0.0077818381   0.013705023    0.0016560774 
+     14000          33   0.0062802433   0.0071774209   0.013989711    0.0022456467 
+     14100          33   0.0061284367   0.0070039277   0.014073612    0.0018742857 
+     14200          33   0.0057433035   0.0065637755   0.014047397    0.0020392999 
+     14300          33   0.0063090214   0.0072103102   0.014753175    0.0021809345 
+     14400          33   0.0063433397   0.0072495311   0.015426943    0.002500832  
+     14500          32   0.0061158095   0.0070218553   0.015950673    0.0027020781 
+     14600          32   0.0062066544   0.0071261588   0.016604099    0.0030376405 
+     14700          32   0.0065514445   0.0075220288   0.017446154    0.0034215744 
+     14800          32   0.0064362118   0.0073897247   0.018112867    0.0060394662 
+     14900          32   0.0062716467   0.0072007796   0.018677808    0.0042404649 
+     15000          32   0.0062889642   0.0072206626   0.019444241    0.0047535052 
+Loop time of 0.260637 on 4 procs for 5000 steps with 32 atoms
+
+Performance: 8287379.423 tau/day, 19183.749 timesteps/s, 613.880 katom-step/s
+90.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0026733  | 0.0039641  | 0.0061372  |   2.1 |  1.52
+Neigh   | 0.00031681 | 0.00038237 | 0.00048999 |   0.0 |  0.15
+Comm    | 0.026111   | 0.028098   | 0.029126   |   0.7 | 10.78
+Output  | 0.12793    | 0.16614    | 0.22099    |   8.9 | 63.74
+Modify  | 0.0021853  | 0.0026076  | 0.0032592  |   0.8 |  1.00
+Other   |            | 0.05944    |            |       | 22.81
+
+Nlocal:              8 ave          13 max           6 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost:             24 ave          26 max          19 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 72
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.surf.stl.g++.1

@@ -0,0 +1,338 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  1 by 1 by 1 MPI processor grid
+
+fix             20 all surface/local surf.tri.stl
+Reading STL object STL version of surf.tri from text file surf.tri.stl
+set             type 1 type 2
+Setting atom values ...
+  4 settings made for type
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.33 | 13.33 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95089817     1.0393538      0.51608705     0.025335722  
+       600          48   0.83949391     0.91758637     0.46172806     0.022515854  
+       700          48   0.8600588      0.94006427     0.48254195     0.046349308  
+       800          48   0.72636179     0.79393033     0.42561821     0.02213745   
+       900          72   0.68028474     0.72089876     0.37868178     0.028124504  
+      1000          72   0.59827548     0.63399342     0.33666552     0.057932603  
+      1100          72   0.60134295     0.63724402     0.3383098      0.025565346  
+      1200          72   0.58062156     0.61528554     0.33134629     0.031222266  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.43299069     0.45289831     0.24603739     0.033378543  
+      1400          92   0.48785257     0.51028258     0.27462447     0.029606478  
+      1500          92   0.50410905     0.52728648     0.28580371     0.031570548  
+      1600          92   0.44335358     0.46373765     0.25474076     0.025856762  
+      1700         104   0.31258594     0.32521568     0.18562847     0.056917788  
+      1800         104   0.29652255     0.30850326     0.17882758     0.036853847  
+      1900         104   0.2438002      0.25365071     0.15147734     0.027067985  
+      2000         104   0.20778515     0.21618051     0.12797216     0.024491014  
+      2100         104   0.23803938     0.24765713     0.13878356     0.018557519  
+      2200         104   0.22477903     0.23386101     0.13254455     0.034204374  
+      2300         103   0.11028018     0.11478141     0.071880248    0.023107934  
+      2400         103   0.051939416    0.054059392    0.04238437     0.010076125  
+      2500         103   0.04046389     0.042115477    0.03276739     0.0092675482 
+      2600         102   0.034504146    0.035926998    0.027152703    0.012043982  
+      2700         102   0.029660748    0.030883871    0.023043461    0.0098675596 
+      2800         102   0.023675472    0.02465178     0.018814934    0.0079223517 
+      2900         102   0.01955555     0.020361964    0.015095009    0.010178019  
+      3000         101   0.010976926    0.011434298    0.0094599476   0.0062989926 
+      3100         101   0.010404873    0.01083841     0.0088413578   0.006904568  
+      3200         101   0.0084790802   0.0088323752   0.0067474787   0.0078181584 
+      3300         101   0.0049651339   0.0051720145   0.0045655092   0.0077852556 
+      3400         101   0.0028770081   0.0029968834   0.0028180577   0.0065531061 
+      3500         101   0.0026603851   0.0027712345   0.0026301508   0.0066265532 
+      3600         100   0.0022879435   0.002384278    0.0022868891   0.005946377  
+      3700         100   0.0020797371   0.002167305    0.0021366338   0.0060275426 
+      3800         100   0.0018223254   0.0018990549   0.0018542925   0.0058665012 
+      3900         100   0.0016056933   0.0016733014   0.0017380009   0.0065755667 
+      4000         100   0.0012764017   0.001330145    0.0014831053   0.0057002441 
+      4100         100   0.0011732772   0.0012226783   0.0014520833   0.0058997102 
+      4200         100   0.0011509224   0.0011993823   0.0014499925   0.005891705  
+      4300         100   0.00093450709  0.00097385475  0.0011305405   0.0060755638 
+      4400         100   0.00073710728  0.00076814338  0.00093491029  0.005994252  
+      4500         100   0.00066950467  0.00069769434  0.00081329183  0.0060209889 
+      4600         100   0.00067057619  0.00069881097  0.00081870364  0.0066002598 
+      4700         100   0.00061522957  0.00064113397  0.0007867969   0.0061000762 
+      4800         100   0.00057127674  0.0005953305   0.00078435449  0.006075934  
+      4900         100   0.00048538112  0.00050581822  0.00067082262  0.0061360807 
+      5000         100   0.00049531306  0.00051616835  0.00070658811  0.0061425578 
+Loop time of 0.239342 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 9024730.054 tau/day, 20890.579 timesteps/s, 2.089 Matom-step/s
+88.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.026886   | 0.026886   | 0.026886   |   0.0 | 11.23
+Neigh   | 0.0086276  | 0.0086276  | 0.0086276  |   0.0 |  3.60
+Comm    | 0.00041811 | 0.00041811 | 0.00041811 |   0.0 |  0.17
+Output  | 0.19004    | 0.19004    | 0.19004    |   0.0 | 79.40
+Modify  | 0.012242   | 0.012242   | 0.012242   |   0.0 |  5.11
+Other   |            | 0.001133   |            |       |  0.47
+
+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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 320
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.46 | 14.46 | 14.46 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00049531306  0.00051616835  0.00070658811  0.0061401156 
+      5100         100   0.51797813     0.029144789    0.028561434    0.061796302  
+      5200          99   0.53766867     0.044472871    0.048736594    0.052595853  
+      5300          98   0.54821886     0.050173651    0.052878851    0.060444985  
+      5400          95   0.56483365     0.050925371    0.053737351    0.057837587  
+      5500          95   0.56809688     0.054333638    0.055612067    0.043728998  
+      5600          92   0.58741732     0.056826396    0.056374971    0.039138605  
+      5700          92   0.59268005     0.062331088    0.059265481    0.035680319  
+      5800          88   0.62103092     0.066489286    0.060222709    0.035282967  
+      5900          88   0.62345455     0.069029715    0.0628021      0.035017077  
+      6000          85   0.64509294     0.070959095    0.06202824     0.035049999  
+      6100          84   0.65441054     0.07348095     0.062757785    0.035609875  
+      6200          81   0.67575597     0.07301839     0.059946946    0.034382094  
+      6300          80   0.68384452     0.073501833    0.059856228    0.03514656   
+      6400          78   0.7013697      0.075265575    0.059538181    0.034094416  
+      6500          78   0.70386686     0.077899568    0.06122273     0.034195388  
+      6600          77   0.7136876      0.079571915    0.062523938    0.034262144  
+      6700          75   0.73326389     0.082149266    0.061775684    0.036880856  
+      6800          74   0.74125199     0.081163997    0.060577178    0.034065559  
+      6900          73   0.74794382     0.078542284    0.058822059    0.034265565  
+      7000          72   0.75869051     0.0799395      0.060173988    0.03372964   
+      7100          71   0.76478565     0.076119935    0.058622864    0.033529799  
+      7200          70   0.77534407     0.076733249    0.059389913    0.033359627  
+      7300          69   0.78737597     0.078601354    0.060601057    0.03387736   
+      7400          68   0.79334599     0.073700033    0.058720823    0.033449993  
+      7500          65   0.82643666     0.07301444     0.057725758    0.033058102  
+      7600          64   0.83647393     0.070962335    0.057196688    0.034325146  
+      7700          64   0.83136046     0.065502199    0.054505995    0.033284476  
+      7800          63   0.84413416     0.065952385    0.055713645    0.032527019  
+      7900          63   0.84474799     0.066608547    0.057188344    0.032380197  
+      8000          63   0.84601678     0.067964843    0.059162055    0.035623321  
+      8100          62   0.85442995     0.063318376    0.056917075    0.033794671  
+      8200          60   0.87886485     0.060762667    0.053902381    0.031778389  
+      8300          60   0.88023598     0.062233516    0.05567968     0.032190408  
+      8400          58   0.91091634     0.064361351    0.056842653    0.031999455  
+      8500          58   0.91076207     0.064195441    0.056598399    0.031981767  
+      8600          57   0.92732215     0.065749251    0.058085176    0.031964139  
+      8700          56   0.94060812     0.063183664    0.057132444    0.031795486  
+      8800          54   0.97102642     0.060271847    0.054931651    0.031534156  
+      8900          53   0.98835079     0.06006587     0.054799498    0.031664682  
+      9000          52   1.0052014      0.058599798    0.0548155      0.031347041  
+      9100          51   1.0232141      0.057600571    0.054358272    0.031293028  
+      9200          51   1.0234203      0.057824665    0.055491376    0.031272133  
+      9300          50   1.0422387      0.056858101    0.055336743    0.031184651  
+      9400          49   1.0607968      0.054708372    0.054237694    0.031018741  
+      9500          49   1.0598447      0.053669652    0.05412067     0.030987958  
+      9600          47   1.0997672      0.049481209    0.049207618    0.030830628  
+      9700          47   1.1009351      0.050760379    0.05160771     0.030681632  
+      9800          46   1.1225281      0.048846024    0.052582727    0.030659518  
+      9900          46   1.1235541      0.049972117    0.054322137    0.030823675  
+     10000          43   1.1964897      0.045828636    0.049253726    0.03048984   
+Loop time of 0.22501 on 1 procs for 5000 steps with 43 atoms
+
+Performance: 9599559.914 tau/day, 22221.204 timesteps/s, 955.512 katom-step/s
+89.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.023112   | 0.023112   | 0.023112   |   0.0 | 10.27
+Neigh   | 0.0050165  | 0.0050165  | 0.0050165  |   0.0 |  2.23
+Comm    | 0.00039113 | 0.00039113 | 0.00039113 |   0.0 |  0.17
+Output  | 0.18353    | 0.18353    | 0.18353    |   0.0 | 81.56
+Modify  | 0.011974   | 0.011974   | 0.011974   |   0.0 |  5.32
+Other   |            | 0.0009874  |            |       |  0.44
+
+Nlocal:             43 ave          43 max          43 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 208
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  39 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.58 | 13.58 | 13.58 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          43   0.041464004    0.045828636    0.049253726    0.002992911  
+     10100          43   0.01536718     0.016984778    0.018346335    0.0026107883 
+     10200          43   0.013276935    0.014674507    0.018130285    0.0032805934 
+     10300          43   0.012643213    0.013974077    0.019027228    0.0020933246 
+     10400          43   0.012779466    0.014124673    0.019370488    0.0026402198 
+     10500          43   0.012399341    0.013704535    0.019539407    0.0022259887 
+     10600          43   0.012201003    0.013485319    0.018098349    0.0024634333 
+     10700          43   0.012655256    0.013987388    0.019496323    0.002221395  
+     10800          43   0.012579162    0.013903285    0.019865363    0.0032621089 
+     10900          43   0.012810408    0.014158872    0.020704867    0.0024564532 
+     11000          43   0.013492114    0.014912337    0.020426966    0.0021076994 
+     11100          43   0.012081727    0.013353488    0.019941305    0.0027605259 
+     11200          43   0.011157364    0.012331823    0.019789593    0.0022805894 
+     11300          43   0.011311656    0.012502357    0.020672585    0.0045512862 
+     11400          43   0.010835381    0.011975948    0.019984802    0.002500184  
+     11500          43   0.010883617    0.012029261    0.020161482    0.0024288947 
+     11600          43   0.010601773    0.011717749    0.02043478     0.002518671  
+     11700          43   0.010652376    0.011773679    0.020877142    0.0047191948 
+     11800          43   0.010586149    0.01170048     0.021045412    0.0029958449 
+     11900          42   0.010310675    0.011425342    0.020890641    0.0041299678 
+     12000          42   0.0096193697   0.010659302    0.01734171     0.0055638559 
+     12100          42   0.0090012199   0.0099743248   0.015925878    0.0062568296 
+     12200          42   0.0092694202   0.01027152     0.016223404    0.0031650129 
+     12300          41   0.009275497    0.010306108    0.016491126    0.0051047425 
+     12400          40   0.010347045    0.011529564    0.01780755     0.0020187837 
+     12500          40   0.010872959    0.012115582    0.018095787    0.0017574207 
+     12600          39   0.0094147621   0.010522381    0.018210318    0.0017051826 
+     12700          39   0.0086581705   0.0096767788   0.018566587    0.0018394808 
+     12800          39   0.0082190204   0.009185964    0.018898421    0.003442822  
+     12900          39   0.0078768039   0.0088034867   0.019645193    0.0024525382 
+     13000          39   0.0066934943   0.0074809642   0.016840831    0.0042565543 
+     13100          38   0.0063530854   0.0071231563   0.015836167    0.0033482203 
+     13200          38   0.0067586397   0.0075778688   0.016370483    0.0027718974 
+     13300          37   0.0062831006   0.0070684882   0.016770756    0.0028166814 
+     13400          36   0.005492839    0.0062015924   0.01655756     0.0041562248 
+     13500          36   0.0052681628   0.0059479258   0.011983298    0.0035740396 
+     13600          36   0.0053786817   0.0060727051   0.011670978    0.004098456  
+     13700          36   0.0055059193   0.0062163605   0.01170773     0.0023640523 
+     13800          35   0.0055296574   0.0062669451   0.0119576      0.0031972222 
+     13900          34   0.0052354859   0.0059576219   0.012092776    0.0016695231 
+     14000          33   0.0050682191   0.0057922504   0.01250025     0.0015032079 
+     14100          33   0.0051315263   0.0058646015   0.01289725     0.0014073536 
+     14200          33   0.005254278    0.0060048892   0.012894635    0.0014096146 
+     14300          33   0.0057832225   0.0066093971   0.013867573    0.001419376  
+     14400          33   0.0058060441   0.006635479    0.014475826    0.0025855623 
+     14500          33   0.0058141643   0.0066447593   0.015171174    0.0024244841 
+     14600          32   0.0055995745   0.0064291411   0.016022968    0.0014230432 
+     14700          32   0.0055988198   0.0064282746   0.016907696    0.0015101902 
+     14800          32   0.0057678876   0.0066223895   0.017482798    0.0016956915 
+     14900          32   0.0057096482   0.006555522    0.018478553    0.0019276435 
+     15000          32   0.0057085079   0.0065542128   0.017574244    0.0021196367 
+Loop time of 0.17974 on 1 procs for 5000 steps with 32 atoms
+
+Performance: 12017358.941 tau/day, 27817.961 timesteps/s, 890.175 katom-step/s
+86.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.011735   | 0.011735   | 0.011735   |   0.0 |  6.53
+Neigh   | 0.00083073 | 0.00083073 | 0.00083073 |   0.0 |  0.46
+Comm    | 0.00027647 | 0.00027647 | 0.00027647 |   0.0 |  0.15
+Output  | 0.1603     | 0.1603     | 0.1603     |   0.0 | 89.19
+Modify  | 0.0058558  | 0.0058558  | 0.0058558  |   0.0 |  3.26
+Other   |            | 0.0007393  |            |       |  0.41
+
+Nlocal:             32 ave          32 max          32 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 73
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tri.gran.surf.stl.g++.4

@@ -0,0 +1,339 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -7 7 -7 7 0 9 units box
+create_box      2 box
+Created orthogonal box = (-7 -7 0) to (7 7 9)
+  2 by 2 by 1 MPI processor grid
+
+fix             20 all surface/local surf.tri.stl
+Reading STL object STL version of surf.tri from text file surf.tri.stl
+set             type 1 type 2
+Setting atom values ...
+  4 settings made for type
+
+pair_style	hybrid gran/hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke/history
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+4 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 7 9 units box
+fix             ins sphere pour 100 1 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+Particle insertion: 24 every 400 steps, 100 by step 1601
+
+fix             wall sphere wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 1                 zcylinder 7.0
+
+timestep	0.005
+
+compute         1 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 4 4 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke/history, perpetual, skip trim from (3)
+      attributes: half, newton on, size, history, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.47 | 12.69 | 13.35 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           4   0              0              0              0            
+       100          28   0.36763289     0.43156905     0.21119336     0.005627034  
+       200          28   0.62433559     0.73291569     0.35866087     0.009556157  
+       300          28   0.95860848     1.125323       0.55068998     0.014672579  
+       400          28   1.3704516      1.608791       0.78728068     0.020976299  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       500          48   0.95089817     1.0393538      0.51608705     0.025335722  
+       600          48   0.83949391     0.91758637     0.46172806     0.022515854  
+       700          48   0.8600588      0.94006427     0.48254195     0.046349308  
+       800          48   0.72636179     0.79393033     0.42561821     0.02213745   
+       900          72   0.68028474     0.72089876     0.37868178     0.028124504  
+      1000          72   0.59827548     0.63399342     0.33666552     0.057932603  
+      1100          72   0.60134295     0.63724402     0.3383098      0.025565346  
+      1200          72   0.58062156     0.61528554     0.33134629     0.031222266  
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1300          92   0.43299069     0.45289831     0.24603739     0.033378543  
+      1400          92   0.48785257     0.51028258     0.27462447     0.029606478  
+      1500          92   0.50410905     0.52728648     0.28580371     0.031570548  
+      1600          92   0.44335358     0.46373765     0.25474076     0.025856762  
+      1700         104   0.31258594     0.32521568     0.18562847     0.056917788  
+      1800         104   0.29652255     0.30850326     0.17882758     0.036853847  
+      1900         104   0.2438002      0.25365071     0.15147734     0.027067985  
+      2000         104   0.20778515     0.21618051     0.12797216     0.024491012  
+      2100         104   0.23803938     0.24765713     0.13878356     0.018557518  
+      2200         104   0.22477903     0.23386101     0.13254455     0.034204387  
+      2300         103   0.11028018     0.11478141     0.071880246    0.023108123  
+      2400         103   0.051939196    0.054059163    0.042383035    0.0100614    
+      2500         103   0.040442247    0.042092951    0.032749381    0.01046781   
+      2600         102   0.034504426    0.035927289    0.027149368    0.012010718  
+      2700         102   0.029679791    0.0309037      0.023036586    0.010355503  
+      2800         102   0.023702803    0.024680238    0.018826345    0.007910395  
+      2900         102   0.019561868    0.020368542    0.015101556    0.010178779  
+      3000         101   0.010990893    0.011448847    0.0094754992   0.0063202976 
+      3100         101   0.010529472    0.0109682      0.0089009784   0.007388411  
+      3200         101   0.0084987177   0.0088528309   0.0067377904   0.0075443377 
+      3300         101   0.004926689    0.0051319677   0.0045207553   0.0078470774 
+      3400         101   0.0028833468   0.0030034862   0.0028132775   0.007922942  
+      3500         101   0.0026928316   0.0028050329   0.0026351323   0.0069014836 
+      3600         100   0.0022956296   0.0023922877   0.0022701552   0.0059851937 
+      3700         100   0.0021025959   0.0021911262   0.0021280497   0.0060105187 
+      3800         100   0.0018494532   0.0019273249   0.0018855471   0.0061456458 
+      3900         100   0.0016137385   0.0016816854   0.0017223036   0.0066454899 
+      4000         100   0.0013124128   0.0013676723   0.0014840612   0.0062470481 
+      4100         100   0.0012105075   0.0012614763   0.0014645791   0.0057688838 
+      4200         100   0.0011433138   0.0011914533   0.0014435934   0.0059579374 
+      4300         100   0.00098204031  0.0010233894   0.0012522874   0.0059816181 
+      4400         100   0.00076296239  0.00079508712  0.0009721438   0.0060246257 
+      4500         100   0.00066335366  0.00069128434  0.00091049427  0.006214887  
+      4600         100   0.00062039452  0.0006465164   0.00082139977  0.0060745906 
+      4700         100   0.00062069669  0.00064683129  0.00083492397  0.0064522652 
+      4800         100   0.00050639953  0.00052772161  0.00074517777  0.0062114309 
+      4900         100   0.00048181752  0.00050210458  0.00072773699  0.0061746147 
+      5000         100   0.00045281738  0.00047188337  0.00072834743  0.0067103321 
+Loop time of 0.32014 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 6747055.869 tau/day, 15618.185 timesteps/s, 1.562 Matom-step/s
+93.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0086319  | 0.0091611  | 0.0095994  |   0.4 |  2.86
+Neigh   | 0.003158   | 0.0033497  | 0.0035467  |   0.3 |  1.05
+Comm    | 0.052557   | 0.053497   | 0.054748   |   0.3 | 16.71
+Output  | 0.14638    | 0.18444    | 0.24257    |   8.9 | 57.61
+Modify  | 0.0073375  | 0.011745   | 0.014473   |   2.7 |  3.67
+Other   |            | 0.05795    |            |       | 18.10
+
+Nlocal:             25 ave          27 max          23 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:             75 ave          77 max          73 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 319
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00045281738  0.00047188337  0.00072834743  0.0066020848 
+      5100         100   0.51860744     0.029800601    0.029304106    0.051905706  
+      5200          98   0.53862917     0.040171507    0.047791716    0.050757979  
+      5300          96   0.55112647     0.042263021    0.050195999    0.04601151   
+      5400          93   0.56728592     0.04180938     0.050815028    0.037450075  
+      5500          93   0.56916149     0.043770195    0.053081459    0.03605744   
+      5600          91   0.58284551     0.045872284    0.05148537     0.033849288  
+      5700          90   0.59267876     0.049850941    0.05375731     0.035005112  
+      5800          86   0.61680698     0.04836437     0.052582503    0.033850751  
+      5900          85   0.62574796     0.050646859    0.054238313    0.034443643  
+      6000          82   0.64727841     0.050889245    0.052494508    0.033866734  
+      6100          80   0.66364069     0.052220462    0.052387252    0.033487505  
+      6200          78   0.67959846     0.052301399    0.050336285    0.033168524  
+      6300          78   0.6815537      0.054363773    0.051168788    0.033400067  
+      6400          76   0.69757373     0.053619014    0.048730817    0.033079249  
+      6500          76   0.69960717     0.055767015    0.050448147    0.034190142  
+      6600          75   0.71046572     0.05804834     0.050353278    0.033120738  
+      6700          73   0.73004213     0.059587557    0.050356776    0.033203715  
+      6800          72   0.73955244     0.059658858    0.049165521    0.033090601  
+      6900          72   0.73984252     0.05996626     0.04893239     0.03538438   
+      7000          72   0.73855905     0.05860616     0.048218057    0.032977368  
+      7100          71   0.74996747     0.060403683    0.049738231    0.032942299  
+      7200          71   0.74958163     0.059994462    0.04984795     0.034576756  
+      7300          71   0.74958014     0.059992886    0.050595934    0.033560699  
+      7400          69   0.77040618     0.060570951    0.05074398     0.032817955  
+      7500          68   0.78190055     0.061527899    0.051576944    0.032829232  
+      7600          67   0.79252938     0.061223545    0.051664985    0.033139179  
+      7700          67   0.79257577     0.061272925    0.052020235    0.032808213  
+      7800          67   0.79235064     0.06103327     0.052983733    0.032695163  
+      7900          65   0.81235659     0.057995702    0.051797211    0.032371751  
+      8000          65   0.81047528     0.05598897     0.051741533    0.032279411  
+      8100          63   0.83302221     0.054074089    0.049909885    0.03200106   
+      8200          62   0.84514204     0.053378682    0.050396436    0.032363269  
+      8300          61   0.85723702     0.052198956    0.049950193    0.031878528  
+      8400          60   0.86997524     0.051226536    0.050780002    0.031636653  
+      8500          60   0.86954615     0.050766237    0.051169838    0.036559517  
+      8600          58   0.89936909     0.051942618    0.050191748    0.037496085  
+      8700          58   0.89897047     0.05151391     0.051173535    0.034671574  
+      8800          56   0.93013263     0.051886568    0.052056826    0.031441238  
+      8900          55   0.94599772     0.051455942    0.052973742    0.034207698  
+      9000          53   0.97967117     0.050662944    0.052877672    0.035867184  
+      9100          51   1.0142291      0.047834254    0.050461469    0.032649796  
+      9200          50   1.033876       0.047752147    0.050703363    0.030822387  
+      9300          49   1.0547579      0.04812047     0.050590947    0.030893945  
+      9400          49   1.0558051      0.049262873    0.052436796    0.030873639  
+      9500          48   1.0767984      0.048801088    0.051653283    0.030786358  
+      9600          46   1.1213506      0.047553612    0.049643046    0.030642108  
+      9700          46   1.1227493      0.049088768    0.051778335    0.030603423  
+      9800          45   1.1452146      0.046959031    0.051250902    0.032613968  
+      9900          45   1.1460384      0.047865295    0.05426893     0.036176412  
+     10000          44   1.1711564      0.047401187    0.054529055    0.033327294  
+Loop time of 0.28856 on 4 procs for 5000 steps with 44 atoms
+
+Performance: 7485434.832 tau/day, 17327.395 timesteps/s, 762.405 katom-step/s
+91.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0077008  | 0.0081727  | 0.0083688  |   0.3 |  2.83
+Neigh   | 0.0016509  | 0.0017298  | 0.0017932  |   0.1 |  0.60
+Comm    | 0.040346   | 0.041058   | 0.041497   |   0.2 | 14.23
+Output  | 0.13753    | 0.1727     | 0.22758    |   8.6 | 59.85
+Modify  | 0.0052102  | 0.0053564  | 0.0055804  |   0.2 |  1.86
+Other   |            | 0.05955    |            |       | 20.64
+
+Nlocal:             11 ave          14 max           9 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:             33 ave          35 max          30 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 181
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  40 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 13.71 | 13.71 | 13.72 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000          44   0.042991774    0.047401187    0.054529055    0.005835563  
+     10100          44   0.017515048    0.019311463    0.022242125    0.0054597963 
+     10200          44   0.016651387    0.018359221    0.021768919    0.007426361  
+     10300          43   0.016651808    0.01840463     0.019841598    0.0053906984 
+     10400          43   0.014274557    0.015777142    0.019217385    0.0055709619 
+     10500          43   0.013716602    0.015160455    0.019335926    0.005533805  
+     10600          43   0.012929871    0.01429091     0.019961256    0.0055113819 
+     10700          43   0.013249241    0.014643898    0.020488568    0.0057553732 
+     10800          43   0.010645141    0.011765682    0.020018164    0.0070545501 
+     10900          43   0.010177915    0.011249275    0.019638619    0.0090787871 
+     11000          43   0.010174433    0.011245426    0.019566189    0.0093512809 
+     11100          43   0.011130765    0.012302425    0.020051358    0.0093282449 
+     11200          42   0.011178858    0.012387383    0.020957174    0.0087638823 
+     11300          42   0.011335071    0.012560484    0.019605652    0.0085884944 
+     11400          42   0.00892055     0.0098849338   0.017254178    0.0115493    
+     11500          42   0.0087305707   0.0096744162   0.016920618    0.0072562207 
+     11600          42   0.0085763835   0.0095035601   0.016735424    0.0073524491 
+     11700          42   0.0091445266   0.010133124    0.016871267    0.0053996766 
+     11800          41   0.0079999518   0.0088888353   0.016813209    0.0052166459 
+     11900          41   0.0079421236   0.0088245818   0.01747319     0.0051109817 
+     12000          41   0.0075832184   0.0084257982   0.016889505    0.0064088798 
+     12100          40   0.0080007752   0.0089151496   0.017619052    0.005204876  
+     12200          40   0.0084961277   0.0094671138   0.0182733      0.007442812  
+     12300          40   0.0098721644   0.011000412    0.019497465    0.0058554546 
+     12400          39   0.0073872276   0.0082563132   0.017957824    0.0074206067 
+     12500          39   0.0074959064   0.0083777777   0.018236089    0.0083410154 
+     12600          39   0.0079646034   0.0089016156   0.018386853    0.010366406  
+     12700          38   0.007907691    0.008866199    0.013301549    0.002231989  
+     12800          37   0.0076214799   0.0085741649   0.013938502    0.0020598491 
+     12900          36   0.00691836     0.0078110516   0.013261785    0.0019344109 
+     13000          36   0.0063774393   0.0072003347   0.011546252    0.0021781987 
+     13100          35   0.0065688938   0.0074447463   0.011179758    0.0018476982 
+     13200          35   0.006608481    0.0074896118   0.011296542    0.0028753707 
+     13300          35   0.0070429905   0.007982056    0.011580455    0.0017137712 
+     13400          35   0.0069974233   0.007930413    0.011637164    0.0017013866 
+     13500          35   0.0070448152   0.0079841239   0.012227322    0.0016768457 
+     13600          35   0.0070302138   0.0079675757   0.012851645    0.0016524347 
+     13700          35   0.0070610122   0.0080024805   0.013351059    0.0016599408 
+     13800          35   0.0068527095   0.0077664041   0.013322016    0.0021396807 
+     13900          35   0.0068663277   0.0077818381   0.013705023    0.0016560774 
+     14000          33   0.0062802433   0.0071774209   0.013989711    0.0022456467 
+     14100          33   0.0061284367   0.0070039277   0.014073612    0.0018742857 
+     14200          33   0.0057433035   0.0065637755   0.014047397    0.0020392999 
+     14300          33   0.0063090214   0.0072103102   0.014753175    0.0021809345 
+     14400          33   0.0063433397   0.0072495311   0.015426943    0.002500832  
+     14500          32   0.0061158095   0.0070218553   0.015950673    0.0027020781 
+     14600          32   0.0062066544   0.0071261588   0.016604099    0.0030376405 
+     14700          32   0.0065514445   0.0075220288   0.017446154    0.0034215744 
+     14800          32   0.0064362118   0.0073897247   0.018112867    0.0060394662 
+     14900          32   0.0062716467   0.0072007796   0.018677808    0.0042404649 
+     15000          32   0.0062889642   0.0072206626   0.019444241    0.0047535052 
+Loop time of 0.255191 on 4 procs for 5000 steps with 32 atoms
+
+Performance: 8464239.384 tau/day, 19593.147 timesteps/s, 626.981 katom-step/s
+93.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0027149  | 0.0039748  | 0.0060577  |   2.0 |  1.56
+Neigh   | 0.00031285 | 0.00037907 | 0.00047986 |   0.0 |  0.15
+Comm    | 0.026002   | 0.02773    | 0.02888    |   0.7 | 10.87
+Output  | 0.12772    | 0.16234    | 0.21585    |   8.7 | 63.62
+Modify  | 0.0022056  | 0.0026604  | 0.0032387  |   0.7 |  1.04
+Other   |            | 0.05811    |            |       | 22.77
+
+Nlocal:              8 ave          13 max           6 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost:             24 ave          26 max          19 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 72
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gransurf/log.1Jul24.tribox.gran.data.g++.1

@@ -0,0 +1,527 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tribox
+Reading data file ...
+  orthogonal box = (-9 -9 -9) to (9 9 9)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  24 atoms
+  24 triangles
+  read_data CPU = 0.001 seconds
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.31 | 7.31 | 7.31 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0039968633 
+       200          54   0.65485258     1.1967995      0.5882574      0.0059511637 
+       300          54   0.70130448     1.2816944      0.63007607     0.0063733089 
+       400          54   0.45082726     0.82392569     0.41204308     0.0042712044 
+       500          54   0.42703582     0.78044477     0.38975619     0.0078751113 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.36378363     0.50236787     0.26121204     0.005580258  
+       700          88   0.40897553     0.56477573     0.29461507     0.0062103139 
+       800          88   0.45442734     0.62754252     0.32702702     0.01172199   
+       900          88   0.38769052     0.53538215     0.29109526     0.011453827  
+      1000          88   0.37409476     0.51660706     0.2871167      0.0081282082 
+      1100          88   0.35735415     0.49348906     0.27107416     0.0085794315 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.33910268     0.42214823     0.22820948     0.014523415  
+      1300         123   0.34253102     0.42641617     0.23083606     0.012592038  
+      1400         123   0.26380089     0.32840519     0.18540471     0.019217679  
+      1500         123   0.26287435     0.32725175     0.18382847     0.009073899  
+      1600         123   0.22125116     0.27543512     0.15863519     0.011459114  
+      1700         124   0.17994881     0.22357276     0.1323084      0.0048041133 
+      1800         124   0.10484006     0.13025583     0.085106685    0.0044535742 
+      1900         124   0.070460717    0.087542103    0.059477957    0.0027460127 
+      2000         124   0.069140804    0.085902211    0.057177221    0.0028764389 
+      2100         124   0.044395978    0.055158639    0.037361834    0.0047974667 
+      2200         124   0.043165403    0.053629743    0.03447346     0.0026358928 
+      2300         124   0.022301073    0.027707394    0.020102237    0.0014883335 
+      2400         124   0.013514412    0.016790633    0.013186206    0.002325602  
+      2500         124   0.010269497    0.012759072    0.010167755    0.0018750155 
+      2600         124   0.007156998    0.0088920278   0.0079248938   0.0019606606 
+      2700         124   0.0053272592   0.0066187159   0.0060381396   0.0015899189 
+      2800         124   0.0049732574   0.0061788955   0.0055201323   0.0015575098 
+      2900         124   0.0034389569   0.0042726435   0.0040970394   0.0023173363 
+      3000         124   0.0027613458   0.003430763    0.0032325603   0.0018824388 
+      3100         124   0.0024990042   0.0031048234   0.0028215135   0.0026234259 
+      3200         124   0.0017976528   0.0022334474   0.0021940732   0.0016842693 
+      3300         124   0.0010884141   0.001352272    0.0014613478   0.0015441795 
+      3400         124   0.0010405091   0.0012927537   0.0013956745   0.001571443  
+      3500         124   0.0010765766   0.0013375648   0.0013287703   0.0015522494 
+      3600         124   0.00081891021  0.0010174339   0.0011208035   0.0016000812 
+      3700         124   0.00090145807  0.0011199934   0.0011567831   0.0015733122 
+      3800         124   0.00140364     0.0017439164   0.0013153706   0.0017988685 
+      3900         124   0.00049247822  0.00061186688  0.00071870865  0.0015665202 
+      4000         124   0.00045666898  0.00056737661  0.00066940396  0.0015712098 
+      4100         124   0.00042619616  0.00052951644  0.00063332787  0.0015759583 
+      4200         124   0.00036113651  0.00044868475  0.00056665527  0.001576302  
+      4300         124   0.00035226447  0.00043766192  0.00055789831  0.0016105156 
+      4400         124   0.00031038324  0.00038562766  0.00052368731  0.0017233961 
+      4500         124   0.00028932551  0.00035946503  0.00048434265  0.0015563793 
+      4600         124   0.00027970544  0.00034751282  0.00047166992  0.0015933351 
+      4700         124   0.00023781605  0.00029546842  0.0004057567   0.0016542167 
+      4800         124   0.00022258987  0.00027655106  0.00035988265  0.0016019168 
+      4900         124   0.00019863185  0.00024678503  0.000326351    0.0016355539 
+      5000         124   0.00019419048  0.00024126696  0.00031309062  0.0016596206 
+Loop time of 0.391027 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5523915.822 tau/day, 12786.842 timesteps/s, 1.586 Matom-step/s
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.053101   | 0.053101   | 0.053101   |   0.0 | 13.58
+Neigh   | 0.014276   | 0.014276   | 0.014276   |   0.0 |  3.65
+Comm    | 0.00043726 | 0.00043726 | 0.00043726 |   0.0 |  0.11
+Output  | 0.31734    | 0.31734    | 0.31734    |   0.0 | 81.16
+Modify  | 0.0045131  | 0.0045131  | 0.0045131  |   0.0 |  1.15
+Other   |            | 0.001358   |            |       |  0.35
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 271
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.438 | 8.438 | 8.438 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00019419048  0.00024126696  0.00031309062  0.0015836208 
+      5100         124   5.241725       0.14230443     0.084309766    0.11222949   
+      5200         124   5.2642517      0.17029222     0.09711751     0.11218019   
+      5300         124   5.2777919      0.18711487     0.1031694      0.11250066   
+      5400         124   5.2848791      0.19592009     0.10535436     0.11248274   
+      5500         124   5.2950507      0.20855763     0.10994851     0.11343591   
+      5600         124   5.3041095      0.21981245     0.11454068     0.1133945    
+      5700         124   5.3104632      0.2277064      0.1180875      0.11432799   
+      5800         124   5.3215398      0.24146836     0.12466168     0.11484551   
+      5900         124   5.3283998      0.24999131     0.1287391      0.11546725   
+      6000         124   5.3321636      0.25466756     0.13051832     0.11515099   
+      6100         124   5.3345557      0.25763958     0.13171407     0.1154897    
+      6200         124   5.3367433      0.26035754     0.13279725     0.11544669   
+      6300         124   5.3395019      0.26378486     0.13420445     0.11516374   
+      6400         124   5.3439366      0.26929459     0.13696206     0.11652747   
+      6500         124   5.35113        0.27823186     0.14087131     0.11539692   
+      6600         124   5.3551686      0.28324957     0.14315746     0.11583188   
+      6700         124   5.3588826      0.28786385     0.14529906     0.11709354   
+      6800         124   5.3635971      0.29372131     0.14771532     0.11643632   
+      6900         124   5.3683547      0.2996322      0.15048478     0.1161893    
+      7000         124   5.3707971      0.30266678     0.15196892     0.11646592   
+      7100         124   5.3726385      0.30495451     0.15306469     0.11625217   
+      7200         124   5.3744003      0.30714351     0.1541348      0.11686937   
+      7300         124   5.3753054      0.30826801     0.15467201     0.11652641   
+      7400         124   5.3757946      0.30887573     0.15508365     0.11719168   
+      7500         124   5.3758028      0.30888597     0.15505055     0.12000677   
+      7600         124   5.3786577      0.31243298     0.15672307     0.11722909   
+      7700         124   5.3783037      0.31199314     0.15642477     0.11632325   
+      7800         124   5.3796187      0.31362692     0.1572947      0.11713976   
+      7900         124   5.3803155      0.31449269     0.15764005     0.11729058   
+      8000         124   5.3825354      0.31725075     0.15884646     0.11762989   
+      8100         124   5.3825657      0.31728832     0.1588842      0.11758412   
+      8200         124   5.3832535      0.31814284     0.15927407     0.11730022   
+      8300         124   5.3835483      0.31850913     0.15938562     0.1178199    
+      8400         124   5.3845014      0.31969331     0.16005175     0.11728308   
+      8500         124   5.3847484      0.32000021     0.16013165     0.11754726   
+      8600         124   5.3863469      0.32198622     0.16098001     0.11783688   
+      8700         124   5.3860321      0.32159511     0.16070948     0.11787101   
+      8800         124   5.3865227      0.32220457     0.16101193     0.11742856   
+      8900         124   5.386608       0.32231066     0.16107457     0.11751927   
+      9000         124   5.3866344      0.32234342     0.16111142     0.11733366   
+      9100         124   5.3870414      0.32284907     0.16138634     0.11732917   
+      9200         124   5.3872929      0.32316151     0.16152699     0.11720705   
+      9300         124   5.3871547      0.32298987     0.16146033     0.11742964   
+      9400         124   5.3870097      0.32280972     0.16135009     0.11718262   
+      9500         124   5.3871151      0.3229406      0.16142031     0.11740809   
+      9600         124   5.3880467      0.3240981      0.16192517     0.11747626   
+      9700         124   5.3882634      0.32436734     0.16207328     0.11748896   
+      9800         124   5.3885751      0.32475452     0.162293       0.1175098    
+      9900         124   5.388935       0.32520177     0.16248897     0.11781973   
+     10000         124   5.3891679      0.32549112     0.16263293     0.11743863   
+Loop time of 0.415747 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5195465.111 tau/day, 12026.540 timesteps/s, 1.491 Matom-step/s
+98.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.075657   | 0.075657   | 0.075657   |   0.0 | 18.20
+Neigh   | 0.020388   | 0.020388   | 0.020388   |   0.0 |  4.90
+Comm    | 0.00050329 | 0.00050329 | 0.00050329 |   0.0 |  0.12
+Output  | 0.30865    | 0.30865    | 0.30865    |   0.0 | 74.24
+Modify  | 0.0089953  | 0.0089953  | 0.0089953  |   0.0 |  2.16
+Other   |            | 0.001558   |            |       |  0.37
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 315
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.563 | 7.563 | 7.563 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.26198066     0.32549112     0.16263293     0.0055911461 
+     10100         124   0.074481727    0.092537903    0.05769404     0.0057995742 
+     10200         124   0.055374095    0.068798118    0.050803609    0.0039966145 
+     10300         124   0.046890231    0.058257559    0.045562379    0.0045743145 
+     10400         124   0.038619299    0.047981553    0.039858993    0.0037329536 
+     10500         124   0.03109186     0.038629281    0.033475837    0.005404066  
+     10600         124   0.026610842    0.033061955    0.03074617     0.0049940987 
+     10700         124   0.023393335    0.029064446    0.027629225    0.0044956047 
+     10800         124   0.020188452    0.025082623    0.024277568    0.0027508375 
+     10900         124   0.017401987    0.021620651    0.022968471    0.0030526263 
+     11000         124   0.017010388    0.021134118    0.02312837     0.0029423416 
+     11100         124   0.015586659    0.019365243    0.022124516    0.0048751832 
+     11200         124   0.015018747    0.018659656    0.021425944    0.0050256257 
+     11300         124   0.013616167    0.016917056    0.020531515    0.0025382988 
+     11400         124   0.012960825    0.016102844    0.020233716    0.0028514371 
+     11500         124   0.012535764    0.015574737    0.019749488    0.004004479  
+     11600         124   0.012468691    0.015491404    0.020056281    0.0029836259 
+     11700         124   0.010340151    0.012846854    0.016889426    0.002611651  
+     11800         124   0.0094736661   0.011770312    0.016202659    0.0028183754 
+     11900         124   0.0097558259   0.012120875    0.017186585    0.003204093  
+     12000         124   0.0096163767   0.01194762     0.018177114    0.0030658747 
+     12100         124   0.0091146678   0.011324284    0.017747849    0.0029559042 
+     12200         124   0.0085146536   0.010578812    0.01795826     0.0020989622 
+     12300         124   0.008795199    0.010927368    0.017709763    0.0025139035 
+     12400         124   0.0090055902   0.011188764    0.017918106    0.0023682314 
+     12500         124   0.0097315664   0.012090734    0.018823404    0.0020873256 
+     12600         124   0.0091405944   0.011356496    0.017804633    0.0027702904 
+     12700         124   0.0087960463   0.010928421    0.017802652    0.0026273577 
+     12800         124   0.0080743005   0.010031707    0.017331563    0.0020791763 
+     12900         124   0.0076898221   0.0095540215   0.016852716    0.0021221914 
+     13000         124   0.0076710324   0.0095306767   0.016825465    0.0039685383 
+     13100         124   0.0073591325   0.0091431646   0.015871642    0.0027994321 
+     13200         124   0.0072640024   0.0090249727   0.016222349    0.0025128819 
+     13300         124   0.0069183134   0.0085954802   0.016490498    0.0021502501 
+     13400         124   0.0069316499   0.0086120499   0.017605557    0.0018524525 
+     13500         124   0.0068915832   0.00856227     0.017409609    0.0033139311 
+     13600         124   0.0062913693   0.0078165497   0.016392828    0.0024061992 
+     13700         124   0.0068995705   0.0085721937   0.016786658    0.001969641  
+     13800         124   0.0072699745   0.0090323926   0.017042011    0.0027635615 
+     13900         124   0.0068420472   0.0085007253   0.016141459    0.0031252065 
+     14000         124   0.0065644583   0.0081558421   0.016569085    0.002456998  
+     14100         124   0.0061341628   0.0076212326   0.016662644    0.0026875721 
+     14200         124   0.0060909188   0.0075675051   0.015930704    0.0030431779 
+     14300         124   0.0063988636   0.0079501032   0.015828756    0.0025592835 
+     14400         124   0.005689416    0.0070686683   0.015368259    0.0024185934 
+     14500         124   0.006236795    0.0077487453   0.015706212    0.0022824924 
+     14600         124   0.0066260155   0.0082323223   0.015933317    0.0025821009 
+     14700         124   0.0062293355   0.0077394775   0.015731127    0.0024183438 
+     14800         124   0.0058972158   0.0073268438   0.015509568    0.0019834714 
+     14900         124   0.0056540749   0.0070247597   0.015502274    0.0023237962 
+     15000         124   0.0052244823   0.0064910235   0.014736944    0.0020149012 
+Loop time of 0.390059 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5537628.750 tau/day, 12818.585 timesteps/s, 1.590 Matom-step/s
+96.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.061332   | 0.061332   | 0.061332   |   0.0 | 15.72
+Neigh   | 0.0066467  | 0.0066467  | 0.0066467  |   0.0 |  1.70
+Comm    | 0.00038941 | 0.00038941 | 0.00038941 |   0.0 |  0.10
+Output  | 0.31536    | 0.31536    | 0.31536    |   0.0 | 80.85
+Modify  | 0.0049581  | 0.0049581  | 0.0049581  |   0.0 |  1.27
+Other   |            | 0.001377   |            |       |  0.35
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 99
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.438 | 8.438 | 8.438 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0052244823   0.0064910235   0.014736944    0.002027817  
+     15100         124   5.2591096      0.16390347     0.10097318     0.12343593   
+     15200         124   5.3142316      0.23238836     0.13250683     0.11589879   
+     15300         124   5.3197373      0.23922878     0.13533309     0.1229824    
+     15400         124   5.3433084      0.26851411     0.14909465     0.11413727   
+     15500         124   5.3597989      0.28900239     0.1554805      0.11750639   
+     15600         124   5.3732393      0.30570096     0.16312751     0.12186127   
+     15700         124   5.3855061      0.32094152     0.16768264     0.12462102   
+     15800         124   5.3941725      0.33170888     0.17231668     0.12143627   
+     15900         124   5.4009664      0.34014985     0.17546962     0.12765975   
+     16000         124   5.414758       0.3572848      0.18266756     0.12653599   
+     16100         124   5.4175427      0.36074458     0.18432923     0.12774876   
+     16200         124   5.4140092      0.35635451     0.18191261     0.13268443   
+     16300         124   5.4017269      0.34109469     0.17372827     0.1307221    
+     16400         124   5.4017349      0.34110458     0.17298641     0.12625563   
+     16500         124   5.4176382      0.36086328     0.1829199      0.13493836   
+     16600         124   5.4175635      0.36077041     0.1829868      0.12403781   
+     16700         124   5.4214857      0.36564356     0.18548453     0.12740232   
+     16800         124   5.4051413      0.34533679     0.1761884      0.12649075   
+     16900         124   5.3907663      0.32747702     0.16871425     0.12243088   
+     17000         124   5.4230599      0.36759934     0.18961103     0.12160116   
+     17100         124   5.4114147      0.35313105     0.18320073     0.12009866   
+     17200         124   5.4079998      0.34888833     0.182884       0.11676493   
+     17300         124   5.4540074      0.40604927     0.21401186     0.12104014   
+     17400         124   5.5303165      0.50085758     0.26286623     0.1191549    
+     17500         124   5.5799815      0.56256257     0.30155566     0.11936249   
+     17600         123   5.6095354      0.548156       0.29969295     0.11836381   
+     17700         123   5.6162622      0.55653017     0.30689847     0.12651704   
+     17800         123   5.5946219      0.52959016     0.29189633     0.1270846    
+     17900         123   5.6425211      0.58921979     0.32434701     0.12601893   
+     18000         123   5.5850993      0.51773555     0.29149119     0.11855274   
+     18100         123   5.5530995      0.47789905     0.27297395     0.12252876   
+     18200         123   5.5744881      0.5045257      0.28929391     0.12580084   
+     18300         123   5.5264747      0.44475381     0.26170733     0.12122144   
+     18400         123   5.5090751      0.4230932      0.24726654     0.11802832   
+     18500         123   5.4509977      0.35079266     0.21099264     0.11612467   
+     18600         123   5.4202769      0.3125485      0.19482059     0.11897009   
+     18700         123   5.4162186      0.30749631     0.19469653     0.12258369   
+     18800         123   5.4370191      0.33339082     0.21014503     0.12166645   
+     18900         123   5.4341683      0.32984186     0.2060126      0.11734766   
+     19000         123   5.4455201      0.34397369     0.21089269     0.1309388    
+     19100         121   5.5328154      0.34681054     0.21343091     0.11975564   
+     19200         121   5.5203006      0.33116707     0.20004465     0.12011697   
+     19300         120   5.5582048      0.32402462     0.19172463     0.12731511   
+     19400         120   5.5618757      0.32862285     0.19220321     0.13103823   
+     19500         120   5.5815117      0.35321951     0.20143386     0.12608573   
+     19600         120   5.5618845      0.32863386     0.18492513     0.12107732   
+     19700         120   5.5611838      0.32775616     0.18008348     0.12358608   
+     19800         120   5.5537958      0.31850174     0.17451709     0.11885715   
+     19900         120   5.5711779      0.34027514     0.18424588     0.11773742   
+     20000         120   5.5693282      0.33795813     0.1832136      0.11851597   
+Loop time of 0.42962 on 1 procs for 5000 steps with 120 atoms
+
+Performance: 5027701.062 tau/day, 11638.197 timesteps/s, 1.397 Matom-step/s
+96.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.065684   | 0.065684   | 0.065684   |   0.0 | 15.29
+Neigh   | 0.030423   | 0.030423   | 0.030423   |   0.0 |  7.08
+Comm    | 0.0005339  | 0.0005339  | 0.0005339  |   0.0 |  0.12
+Output  | 0.32273    | 0.32273    | 0.32273    |   0.0 | 75.12
+Modify  | 0.0087715  | 0.0087715  | 0.0087715  |   0.0 |  2.04
+Other   |            | 0.001478   |            |       |  0.34
+
+Nlocal:            120 ave         120 max         120 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 433
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  96 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.563 | 7.563 | 7.563 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         120   0.26979851     0.33795813     0.1832136     -0.007144497  
+     20100         120   0.076935724    0.096372118    0.065021814    0.014779222  
+     20200         120   0.068189363    0.08541615     0.058686501    0.0072051902 
+     20300         120   0.072858793    0.091265225    0.059741747    0.0073008259 
+     20400         120   0.064096397    0.080289171    0.054774581    0.013885876  
+     20500         120   0.056290534    0.0705113      0.04961518     0.0011947455 
+     20600         120   0.037451936    0.046913478    0.035446097    0.0046019241 
+     20700         120   0.037362255    0.04680114     0.035577307    0.0068457433 
+     20800         120   0.026254631    0.03288738     0.029046591    0.0072400997 
+     20900         120   0.019914756    0.024945852    0.024193195    0.0086344784 
+     21000         120   0.019965109    0.025008927    0.02348028     0.008745631  
+     21100         120   0.017890973    0.022410798    0.022094331    0.002355569  
+     21200         120   0.018171204    0.022761824    0.021530758    0.0069269189 
+     21300         120   0.016051273    0.020106332    0.019460189    0.0068448898 
+     21400         120   0.015907324    0.019926016    0.017975049    0.008661722  
+     21500         120   0.015802152    0.019794274    0.018060602    0.0025488481 
+     21600         120   0.018428378    0.023083968    0.023151613    0.0061571836 
+     21700         120   0.017193664    0.021537326    0.022957643    0.0070414228 
+     21800         120   0.014270475    0.017875648    0.021240833   -0.0013442377 
+     21900         120   0.013848094    0.01734656     0.020380261    0.0053796285 
+     22000         120   0.012992089    0.016274301    0.021157393    0.0053721355 
+     22100         120   0.014065446    0.017618822    0.020106722    0.0014345844 
+     22200         120   0.010258737    0.012850418    0.016841221    0.01120688   
+     22300         120   0.010211948    0.012791809    0.017093331    0.0078983762 
+     22400         120   0.009548374    0.011960595    0.01734835     0.0038908434 
+     22500         120   0.0085349512   0.010691149    0.016754781   -0.00014023944
+     22600         120   0.0091912138   0.011513205    0.016019636    0.0045956054 
+     22700         120   0.0087672845   0.010982177    0.016081508    0.0071534675 
+     22800         120   0.0091053807   0.011405687    0.01691824     0.0038334511 
+     22900         120   0.0090436037   0.011328304    0.018774987    0.0025693881 
+     23000         120   0.0090306116   0.011312029    0.018062077    0.0044430084 
+     23100         120   0.0077433932   0.0096996189   0.016375491    0.0064193124 
+     23200         120   0.008478267    0.010620145    0.018103983   -0.00085927214
+     23300         120   0.007964293    0.0099763249   0.017453711    0.002148413  
+     23400         120   0.009046906    0.01133244     0.01770639     0.020441698  
+     23500         120   0.0091534944   0.011465956    0.017415455    0.002285878  
+     23600         120   0.007748423    0.0097059193   0.015490839   -0.00020592716
+     23700         120   0.0066912474   0.0083816677   0.014649077    0.006694411  
+     23800         120   0.007247576    0.0090785426   0.01406457     0.0014410036 
+     23900         120   0.0076543035   0.0095880222   0.015050261    0.0097604987 
+     24000         120   0.0072047826   0.0090249382   0.01472033     0.0068222942 
+     24100         120   0.007482661    0.0093730175   0.014902069    0.0075137142 
+     24200         120   0.0068544845   0.0085861437   0.015181158    0.0040487925 
+     24300         120   0.0068959558   0.008638092    0.01593833     0.0042688713 
+     24400         120   0.0071391701   0.0089427499   0.014834245    0.010035527  
+     24500         120   0.0073382922   0.0091921766   0.016818047    0.0041348411 
+     24600         120   0.0071901432   0.0090066004   0.016444181    0.0046487693 
+     24700         120   0.0066092287   0.0082789285   0.016239103    0.0073248869 
+     24800         120   0.0055322913   0.0069299228   0.012402128   -0.0017910989 
+     24900         120   0.0056839126   0.0071198484   0.013482139    0.0041464303 
+     25000         120   0.0043729877   0.0054777425   0.012826668    0.0017027494 
+Loop time of 0.390633 on 1 procs for 5000 steps with 120 atoms
+
+Performance: 5529481.363 tau/day, 12799.725 timesteps/s, 1.536 Matom-step/s
+95.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.059297   | 0.059297   | 0.059297   |   0.0 | 15.18
+Neigh   | 0.011612   | 0.011612   | 0.011612   |   0.0 |  2.97
+Comm    | 0.00039143 | 0.00039143 | 0.00039143 |   0.0 |  0.10
+Output  | 0.31326    | 0.31326    | 0.31326    |   0.0 | 80.19
+Modify  | 0.0047198  | 0.0047198  | 0.0047198  |   0.0 |  1.21
+Other   |            | 0.001351   |            |       |  0.35
+
+Nlocal:            120 ave         120 max         120 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 173
+Dangerous builds = 0
+
+Total wall time: 0:00:02

examples/gransurf/log.1Jul24.tribox.gran.data.g++.4

@@ -0,0 +1,528 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+read_data	data.tribox
+Reading data file ...
+  orthogonal box = (-9 -9 -9) to (9 9 9)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  24 atoms
+  24 triangles
+  read_data CPU = 0.002 seconds
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+fix             fsl all surface/local NULL
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+dump_modify	2 pad 5
+
+run	        5000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.337 | 7.338 | 7.342 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0039968633 
+       200          54   0.65485258     1.1967995      0.5882574      0.0059511637 
+       300          54   0.70118095     1.2814686      0.62987441     0.0063721863 
+       400          54   0.45057814     0.82347039     0.41172861     0.0042376606 
+       500          54   0.42112344     0.76963938     0.38709352     0.0090454068 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.37193184     0.51362016     0.26489933     0.0063964776 
+       700          88   0.41426632     0.57208206     0.29533003     0.0077177976 
+       800          88   0.45653662     0.63045534     0.32753609     0.0071074229 
+       900          88   0.38450697     0.53098581     0.28581676     0.0054070755 
+      1000          88   0.35211843     0.48625879     0.2664603      0.010024316  
+      1100          88   0.36008043     0.49725392     0.27221103     0.0097378018 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.35178839     0.43794065     0.23962027     0.012545089  
+      1300         123   0.35870451     0.44655052     0.24405887     0.008071262  
+      1400         123   0.29688415     0.36959048     0.20759032     0.0090729808 
+      1500         123   0.28867163     0.35936673     0.2015813      0.013634049  
+      1600         123   0.21564484     0.26845583     0.15348181     0.0055206244 
+      1700         124   0.16273805     0.20218969     0.11933334     0.0090883805 
+      1800         124   0.11715078     0.14555097     0.092237668    0.0036976622 
+      1900         124   0.068809053    0.085490035    0.059457412    0.0040593291 
+      2000         124   0.059329987    0.073713014    0.051571621    0.0032183709 
+      2100         124   0.04798502     0.059617753    0.041594025    0.0024460605 
+      2200         124   0.042317183    0.052575894    0.035031437    0.0021126303 
+      2300         124   0.016704259    0.020753776    0.016526748    0.0019895102 
+      2400         124   0.012483958    0.015510372    0.012027988    0.0039777224 
+      2500         124   0.0077840862   0.0096711374   0.0076953511   0.0022728499 
+      2600         124   0.0051798085   0.0064355197   0.0055627076   0.0032961978 
+      2700         124   0.0044257315   0.0054986361   0.0048486212   0.0019272834 
+      2800         124   0.0038110636   0.0047349577   0.004136763    0.0016771472 
+      2900         124   0.0033610006   0.0041757886   0.0037955793   0.0016499842 
+      3000         124   0.0036759439   0.0045670818   0.0039739099   0.0017174386 
+      3100         124   0.004879497    0.0060624054   0.0045976588   0.0017124675 
+      3200         124   0.0033701575   0.0041871654   0.0034848116   0.0016618861 
+      3300         124   0.0031218612   0.0038786761   0.0033303126   0.001663116  
+      3400         124   0.0028009663   0.0034799884   0.0030376486   0.0016166164 
+      3500         124   0.0030247379   0.0037580077   0.0030722102   0.0024345187 
+      3600         124   0.0017951568   0.0022303463   0.0019956461   0.0014714833 
+      3700         124   0.0014929161   0.0018548352   0.0017092596   0.0016423379 
+      3800         124   0.0014239364   0.0017691331   0.0016212959   0.0020903921 
+      3900         124   0.00090885869  0.0011291881   0.0012044307   0.0015442055 
+      4000         124   0.00074121189  0.00092089962  0.0010437154   0.0015483599 
+      4100         124   0.00069161146  0.00085927485  0.00094845915  0.0015120623 
+      4200         124   0.00056635858  0.00070365763  0.00080321665  0.0014656722 
+      4300         124   0.00050531087  0.00062781047  0.00073303224  0.0015267341 
+      4400         124   0.00045239991  0.00056207262  0.00068482519  0.0016991771 
+      4500         124   0.00042229712  0.00052467217  0.00065368139  0.001504402  
+      4600         124   0.00038562197  0.00047910609  0.00061752973  0.0018182444 
+      4700         124   0.00034669692  0.00043074466  0.00057495931  0.0015077949 
+      4800         124   0.00030333089  0.00037686565  0.00052302102  0.0014545772 
+      4900         124   0.00029290547  0.00036391286  0.00051399552  0.0014965779 
+      5000         124   0.00027955382  0.00034732445  0.00049201819  0.0015020264 
+Loop time of 0.439493 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 4914759.070 tau/day, 11376.757 timesteps/s, 1.411 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    | 0.0019905  | 0.016708   | 0.032935   |  11.4 |  3.80
+Neigh   | 0.0018982  | 0.0049817  | 0.007949   |   4.1 |  1.13
+Comm    | 0.067011   | 0.083326   | 0.098679   |   5.1 | 18.96
+Output  | 0.22205    | 0.26015    | 0.32361    |   8.1 | 59.19
+Modify  | 0.0014787  | 0.0027393  | 0.0042002  |   2.4 |  0.62
+Other   |            | 0.07159    |            |       | 16.29
+
+Nlocal:             31 ave          55 max           6 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         118 max          69 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 276
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.614 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00027955382  0.00034732445  0.00049201819  0.0015031883 
+      5100         124   5.2213292      0.11696419     0.070191681    0.11567903   
+      5200         124   5.2494151      0.15185888     0.088948694    0.11228004   
+      5300         124   5.2572413      0.16158228     0.091155723    0.11191697   
+      5400         124   5.2622945      0.16786055     0.091191608    0.11200573   
+      5500         124   5.2694754      0.17678222     0.094474963    0.11274427   
+      5600         124   5.2791339      0.18878212     0.099452746    0.11279348   
+      5700         124   5.2936967      0.20687533     0.10794158     0.11359394   
+      5800         124   5.3074309      0.22393911     0.11535088     0.11345736   
+      5900         124   5.3170002      0.23582815     0.1211834      0.11451637   
+      6000         124   5.3264792      0.24760517     0.12691981     0.11634565   
+      6100         124   5.329844       0.25178562     0.12907012     0.11440026   
+      6200         124   5.3347032      0.25782277     0.13173987     0.11647845   
+      6300         124   5.340892       0.26551199     0.13511823     0.11510697   
+      6400         124   5.3470903      0.27321282     0.13821674     0.11586585   
+      6500         124   5.3530895      0.28066635     0.14158978     0.11592173   
+      6600         124   5.3580451      0.28682334     0.14446804     0.11687967   
+      6700         124   5.3594973      0.28862764     0.14530407     0.11693613   
+      6800         124   5.362035       0.2917805      0.14687648     0.11633757   
+      6900         124   5.3630264      0.29301222     0.14751378     0.11682536   
+      7000         124   5.3660652      0.29678769     0.14942643     0.11653024   
+      7100         124   5.368112       0.29933078     0.15041714     0.11744944   
+      7200         124   5.3687484      0.30012138     0.15086898     0.1169356    
+      7300         124   5.3685878      0.29992191     0.15057777     0.11770109   
+      7400         124   5.3701975      0.3019218      0.15147912     0.11740293   
+      7500         124   5.3710321      0.30295873     0.15204994     0.1177079    
+      7600         124   5.3727095      0.30504273     0.15306656     0.11818598   
+      7700         124   5.3736085      0.30615972     0.15355634     0.11726622   
+      7800         124   5.375909       0.30901792     0.15495105     0.118266     
+      7900         124   5.376276       0.30947392     0.15519466     0.11718369   
+      8000         124   5.3791711      0.31307082     0.15690211     0.11765829   
+      8100         124   5.3787496      0.31254718     0.1566274      0.11760075   
+      8200         124   5.3791354      0.31302651     0.15693452     0.11856675   
+      8300         124   5.3812285      0.31562697     0.15815299     0.11772296   
+      8400         124   5.38166        0.31616311     0.15833869     0.11858638   
+      8500         124   5.3821533      0.31677599     0.15873083     0.11727274   
+      8600         124   5.3822551      0.3169025      0.15879148     0.11800294   
+      8700         124   5.3820649      0.31666611     0.15870109     0.11689663   
+      8800         124   5.3829798      0.31780283     0.15920518     0.11720016   
+      8900         124   5.3847961      0.32005951     0.16021329     0.12034865   
+      9000         124   5.3863825      0.32203038     0.16117074     0.11771618   
+      9100         124   5.3858285      0.32134218     0.16090793     0.1179112    
+      9200         124   5.386223       0.32183231     0.16127025     0.11804752   
+      9300         124   5.3862986      0.32192623     0.16133847     0.11757523   
+      9400         124   5.387428       0.3233294      0.16204845     0.11778809   
+      9500         124   5.389036       0.32532724     0.1628191      0.1189939    
+      9600         124   5.390873       0.32760951     0.16393076     0.11809517   
+      9700         124   5.3902745      0.32686591     0.16360448     0.11797716   
+      9800         124   5.3912122      0.32803095     0.16421139     0.1182008    
+      9900         124   5.3919947      0.32900318     0.16468113     0.11897222   
+     10000         124   5.3938706      0.33133377     0.16573607     0.11850659   
+Loop time of 0.451177 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 4787480.364 tau/day, 11082.130 timesteps/s, 1.374 Matom-step/s
+94.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0055802  | 0.027018   | 0.048894   |  13.0 |  5.99
+Neigh   | 0.001921   | 0.0070952  | 0.012313   |   6.1 |  1.57
+Comm    | 0.077928   | 0.10164    | 0.12495    |   7.2 | 22.53
+Output  | 0.20641    | 0.24209    | 0.30176    |   7.9 | 53.66
+Modify  | 0.0029541  | 0.0044657  | 0.0061323  |   2.2 |  0.99
+Other   |            | 0.06887    |            |       | 15.26
+
+Nlocal:             31 ave          59 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:             93 ave         116 max          65 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 316
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.714 | 7.726 | 7.739 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.26668328     0.33133377     0.16573607     0.017328247  
+     10100         124   0.056200102    0.069824369    0.044872322    0.0039707466 
+     10200         124   0.042267205    0.0525138      0.041203231    0.0044598573 
+     10300         124   0.029663878    0.036855122    0.033120538    0.0070651926 
+     10400         124   0.024669667    0.030650193    0.03033595     0.0041946492 
+     10500         124   0.022848926    0.02838806     0.028689326    0.0030599292 
+     10600         124   0.020458165    0.02541772     0.026302636    0.0058319745 
+     10700         124   0.017807934    0.022125009    0.025740761    0.0027488894 
+     10800         124   0.015035885    0.018680949    0.023588376    0.0022903775 
+     10900         124   0.013888267    0.01725512     0.022440279    0.0027634791 
+     11000         124   0.011608462    0.014422635    0.019348673    0.0045780072 
+     11100         124   0.011162709    0.01386882     0.01849931     0.0023451747 
+     11200         124   0.011086175    0.013773732    0.017917304    0.0024658252 
+     11300         124   0.010190232    0.012660591    0.017180502    0.0020222246 
+     11400         124   0.0097496547   0.012113207    0.016751983    0.0030135131 
+     11500         124   0.0093133921   0.011571184    0.016521609    0.002490532  
+     11600         124   0.0081681115   0.01014826     0.015564426    0.0019455596 
+     11700         124   0.0076826338   0.0095450905   0.015672443    0.0022541556 
+     11800         124   0.0073075107   0.0090790284   0.015351511    0.0032455658 
+     11900         124   0.0075051682   0.0093246029   0.016009774    0.0018035686 
+     12000         124   0.0072372959   0.0089917919   0.015490758    0.0042935815 
+     12100         124   0.006916344    0.0085930334   0.014798831    0.0029189494 
+     12200         124   0.0066805653   0.0083000963   0.014911612    0.0027424779 
+     12300         124   0.0061444991   0.0076340746   0.014460476    0.0030202428 
+     12400         124   0.0061696139   0.0076652778   0.014542082    0.0036198571 
+     12500         124   0.0059365088   0.0073756625   0.014858158    0.0027444353 
+     12600         124   0.0058780839   0.007303074    0.015398698    0.0020529534 
+     12700         124   0.0062768514   0.0077985124   0.015619374    0.0025399066 
+     12800         124   0.0060828914   0.0075575317   0.015305797    0.0025106775 
+     12900         124   0.0059859508   0.0074370904   0.014550513    0.0023214829 
+     13000         124   0.0057442406   0.0071367837   0.014207912    0.0023133715 
+     13100         124   0.0060965462   0.0075744967   0.015121064    0.0022806913 
+     13200         124   0.006511295    0.0080897907   0.015347205    0.0018927714 
+     13300         124   0.0054721076   0.0067986791   0.01358699     0.002764088  
+     13400         124   0.0056662979   0.0070399458   0.01408639     0.0027430251 
+     13500         124   0.0053656855   0.0066664577   0.013407158    0.0038500999 
+     13600         124   0.0053355018   0.0066289568   0.014186081    0.0027071631 
+     13700         124   0.0050751903   0.0063055394   0.014588279    0.0023383507 
+     13800         124   0.0049370805   0.0061339485   0.014929944    0.0025317664 
+     13900         124   0.0051863562   0.0064436546   0.015145572    0.0030657941 
+     14000         124   0.0048799741   0.0060629981   0.014209027    0.003051829  
+     14100         124   0.0045561374   0.0056606556   0.013907584    0.002249473  
+     14200         124   0.0044230598   0.0054953167   0.013901718    0.0038863007 
+     14300         124   0.0042868083   0.0053260345   0.013151104    0.0031267464 
+     14400         124   0.0042395107   0.0052672709   0.012829998    0.0028603263 
+     14500         124   0.0041975299   0.0052151129   0.012763534    0.0023412049 
+     14600         124   0.0045709375   0.0056790436   0.014449848    0.0022069733 
+     14700         124   0.0044899655   0.005578442    0.015608166    0.0020443675 
+     14800         124   0.0042163929   0.0052385487   0.015808795    0.0018318737 
+     14900         124   0.0039866761   0.004953143    0.014823117    0.0024666454 
+     15000         124   0.0041610334   0.0051697688   0.013201413    0.0040669573 
+Loop time of 0.997319 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 2165805.538 tau/day, 5013.439 timesteps/s, 621.666 katom-step/s
+92.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0016601  | 0.045665   | 0.089499   |  20.5 |  4.58
+Neigh   | 0.001147   | 0.0040993  | 0.0071947  |   4.6 |  0.41
+Comm    | 0.17379    | 0.21304    | 0.2523     |   8.3 | 21.36
+Output  | 0.46514    | 0.56417    | 0.70813    |  12.6 | 56.57
+Modify  | 0.0017154  | 0.0051509  | 0.0088501  |   4.6 |  0.52
+Other   |            | 0.1652     |            |       | 16.56
+
+Nlocal:             31 ave          57 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:             93 ave         116 max          67 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 89
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.614 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0041610334   0.0051697688   0.013201413    0.004050505  
+     15100         124   5.23434        0.13312915     0.086755644    0.11559576   
+     15200         124   5.2844675      0.19540875     0.11840085     0.1141468    
+     15300         124   5.3318404      0.25426596     0.14579094     0.11909121   
+     15400         124   5.3303276      0.25238652     0.14369585     0.11823013   
+     15500         124   5.3230136      0.24329933     0.13724045     0.12187991   
+     15600         124   5.3578424      0.28657151     0.15433671     0.12381644   
+     15700         123   5.4013676      0.28900827     0.15453476     0.12259662   
+     15800         123   5.4118019      0.30199797     0.15885725     0.12133482   
+     15900         123   5.4208828      0.31330268     0.16122905     0.12182528   
+     16000         123   5.4281775      0.32238394     0.1649621      0.12339788   
+     16100         123   5.4256507      0.31923831     0.16299633     0.11986599   
+     16200         123   5.4289714      0.32337225     0.16480742     0.12883298   
+     16300         123   5.4369808      0.33334311     0.16946939     0.12452535   
+     16400         123   5.4245634      0.31788472     0.16234678     0.12543716   
+     16500         123   5.3981175      0.28496229     0.14752224     0.12546557   
+     16600         123   5.380002       0.26241035     0.13693027     0.12564509   
+     16700         123   5.3577287      0.23468232     0.12320315     0.12447887   
+     16800         123   5.3887674      0.27332227     0.14161821     0.12558582   
+     16900         123   5.3808542      0.26347121     0.13707725     0.12105334   
+     17000         123   5.3780823      0.26002045     0.13613655     0.11611436   
+     17100         123   5.3680186      0.24749217     0.13202509     0.12050881   
+     17200         123   5.3684375      0.24801367     0.13439899     0.11752469   
+     17300         123   5.4125961      0.3029867      0.16565047     0.11809568   
+     17400         122   5.5149345      0.37796948     0.20589267     0.11706067   
+     17500         122   5.5376072      0.40625192     0.22528229     0.12168884   
+     17600         122   5.594801       0.47759671     0.26839568     0.11784984   
+     17700         122   5.6275885      0.51849664     0.29262051     0.12179888   
+     17800         122   5.6620933      0.5615387      0.32018546     0.13677725   
+     17900         122   5.6781565      0.58157636     0.3344357      0.12144476   
+     18000         122   5.6282244      0.51928991     0.30159388     0.1204454    
+     18100         122   5.586202       0.46687012     0.27307657     0.11222952   
+     18200         122   5.5637664      0.43888345     0.26310303     0.12241507   
+     18300         122   5.5396829      0.40884116     0.24778525     0.1180911    
+     18400         122   5.4933462      0.35103977     0.21102933     0.11419006   
+     18500         122   5.4481058      0.29460584     0.17806848     0.11684132   
+     18600         122   5.4233233      0.26369154     0.16408249     0.1156897    
+     18700         122   5.4169852      0.2557853      0.16164551     0.11432694   
+     18800         122   5.402297       0.23746293     0.15603756     0.11338406   
+     18900         122   5.4104328      0.24761171     0.16157759     0.11644593   
+     19000         122   5.412422       0.25009306     0.16543071     0.12348188   
+     19100         121   5.4546597      0.24911594     0.16510456     0.11730105   
+     19200         121   5.477336       0.27746126     0.17852522     0.12205725   
+     19300         121   5.4969126      0.30193201     0.18816473     0.12510238   
+     19400         121   5.4919974      0.29578804     0.18327042     0.13220061   
+     19500         121   5.5032315      0.30983075     0.18311811     0.12373881   
+     19600         121   5.5150579      0.32461371     0.188055       0.12242899   
+     19700         121   5.5066378      0.31408861     0.17504793     0.11846492   
+     19800         121   5.5088848      0.31689728     0.17340496     0.12928325   
+     19900         121   5.518969       0.3295026      0.17902712     0.12421202   
+     20000         121   5.500687       0.30665007     0.16793997     0.11961173   
+Loop time of 0.846225 on 4 procs for 5000 steps with 121 atoms
+
+Performance: 2552512.312 tau/day, 5908.593 timesteps/s, 714.940 katom-step/s
+93.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.014413   | 0.044158   | 0.072833   |  13.5 |  5.22
+Neigh   | 0.0052624  | 0.017126   | 0.029893   |   8.6 |  2.02
+Comm    | 0.16098    | 0.19782    | 0.23481    |   7.8 | 23.38
+Output  | 0.36418    | 0.45212    | 0.56168    |  11.2 | 53.43
+Modify  | 0.0060017  | 0.0089185  | 0.012537   |   3.0 |  1.05
+Other   |            | 0.1261     |            |       | 14.90
+
+Nlocal:          30.25 ave          70 max           6 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:          90.75 ave         115 max          51 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 397
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  97 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.714 | 7.735 | 7.772 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         121   0.24532005     0.30665007     0.16793997    -0.012946091  
+     20100         121   0.070310831    0.087888539    0.059490062    0.0061478766 
+     20200         121   0.058503348    0.073129185    0.048875925    0.0080927743 
+     20300         121   0.074158085    0.092697606    0.057028332    0.0049379442 
+     20400         121   0.069187269    0.086484086    0.053655733    0.0084660817 
+     20500         121   0.049853491    0.062316864    0.042577287    0.0079711185 
+     20600         121   0.027931559    0.034914449    0.024826071    0.0076385601 
+     20700         121   0.02435771     0.030447138    0.023586479    0.0071381857 
+     20800         121   0.027310414    0.034138017    0.026926085    0.0043612389 
+     20900         121   0.029470455    0.036838069    0.029013973    0.0062985385 
+     21000         121   0.023688651    0.029610814    0.025737577    0.0057806959 
+     21100         121   0.023374366    0.029217957    0.025924122    0.0058256936 
+     21200         121   0.021626125    0.027032657    0.023553381    0.014915428  
+     21300         121   0.021517013    0.026896267    0.022266041    0.004819531  
+     21400         121   0.016777636    0.020972045    0.018448572    0.009234911  
+     21500         121   0.012262338    0.015327922    0.015298231    0.0093816891 
+     21600         121   0.010918726    0.013648408    0.014833772    0.0042474881 
+     21700         121   0.011053972    0.013817464    0.014459702   -0.00021820222
+     21800         121   0.010129668    0.012662085    0.013081406    0.0093930484 
+     21900         121   0.010085003    0.012606253    0.014417094    0.0014178838 
+     22000         121   0.0094973723   0.011871715    0.013900622    0.0093877537 
+     22100         121   0.0080430026   0.010053753    0.013679106    0.011613255  
+     22200         121   0.0084072004   0.010509001    0.016027076    0.0035671687 
+     22300         121   0.0083085041   0.01038563     0.016132368    0.007693786  
+     22400         121   0.0079992179   0.0099990223   0.013265655    0.0073563811 
+     22500         121   0.0075222565   0.0094028207   0.012763827    0.005799044  
+     22600         121   0.0076786112   0.0095982641   0.013866351    0.0030214484 
+     22700         121   0.0075068394   0.0093835492   0.01384418     0.0033702789 
+     22800         121   0.0075163502   0.0093954378   0.01466975     0.0088268737 
+     22900         121   0.0073136786   0.0091420982   0.01666669     0.0020531991 
+     23000         121   0.0065872318   0.0082340397   0.017972587    0.0034194419 
+     23100         121   0.0063174876   0.0078968594   0.017018904    0.0051829986 
+     23200         121   0.0058594142   0.0073242678   0.015780468    0.0093443152 
+     23300         121   0.0050717858   0.0063397323   0.015531664    0.0087588922 
+     23400         121   0.0044421678   0.0055527097   0.014248905    0.010646639  
+     23500         121   0.0052180265   0.0065225331   0.014224204    0.0052692738 
+     23600         121   0.0050225965   0.0062782457   0.013251361    8.1489022e-05
+     23700         121   0.0043059081   0.0053823852   0.012534622    0.011277239  
+     23800         121   0.005020183    0.0062752288   0.013523699    0.0054700239 
+     23900         121   0.0043855799   0.0054819749   0.011206169    0.0045566463 
+     24000         121   0.0046936439   0.0058670549   0.012484576    0.0019612692 
+     24100         121   0.0043263983   0.0054079978   0.011282329    0.011449127  
+     24200         121   0.0046535879   0.0058169849   0.01164271     0.0025540746 
+     24300         121   0.0047667406   0.0059584258   0.012209842    0.010676731  
+     24400         121   0.0051690398   0.0064612997   0.01360687     0.0052054694 
+     24500         121   0.0052783564   0.0065979455   0.015574736    0.0058826112 
+     24600         121   0.0050801526   0.0063501908   0.013665316    0.0068012924 
+     24700         121   0.0045361573   0.0056701966   0.013281602    0.0050417691 
+     24800         121   0.0053013393   0.0066266741   0.012795325    0.0065965543 
+     24900         121   0.0049826013   0.0062282516   0.012373501    0.0044363731 
+     25000         121   0.0047299253   0.0059124066   0.012200307    0.0093926226 
+Loop time of 0.573761 on 4 procs for 5000 steps with 121 atoms
+
+Performance: 3764633.700 tau/day, 8714.430 timesteps/s, 1.054 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    | 0.001103   | 0.024207   | 0.060775   |  16.0 |  4.22
+Neigh   | 0.00084396 | 0.0046703  | 0.010272   |   5.7 |  0.81
+Comm    | 0.096646   | 0.13337    | 0.15528    |   6.6 | 23.25
+Output  | 0.25027    | 0.31495    | 0.39587    |   9.8 | 54.89
+Modify  | 0.0012358  | 0.0031766  | 0.0056404  |   3.5 |  0.55
+Other   |            | 0.09338    |            |       | 16.28
+
+Nlocal:          30.25 ave          66 max           5 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Nghost:          90.75 ave         116 max          55 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 155
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/gransurf/log.1Jul24.tribox.gran.global.g++.1

@@ -0,0 +1,491 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tribox
+Read molecule template tris:
+LAMMPS data file for tri box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  24 triangles with 14 points
+
+fix             20 all surface/global tris hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 1 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 yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.5873 | 0.5873 | 0.5873 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       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   0.82347039     0.82347039     0.41172861     0.0029850802 
+       500          30   0.76963938     0.76963938     0.38709352     0.0042867255 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          64   0.51325196     0.51325196     0.26472957     0.0045780407 
+       700          64   0.57133229     0.57133229     0.29476966     0.0046847812 
+       800          64   0.630634       0.630634       0.32751956     0.0050038133 
+       900          64   0.54233611     0.54233611     0.28819808     0.0052880896 
+      1000          64   0.48543152     0.48543152     0.26491902     0.0064773948 
+      1100          64   0.47303609     0.47303609     0.2578388      0.0057125611 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          99   0.40053109     0.40053109     0.2195167      0.0081778049 
+      1300          99   0.42696772     0.42696772     0.23049402     0.006385146  
+      1400          99   0.37139574     0.37139574     0.20331799     0.0074485307 
+      1500          99   0.33478846     0.33478846     0.18670496     0.0061673941 
+      1600          99   0.29982872     0.29982872     0.16693769     0.0051747985 
+      1700         100   0.2069625      0.2069625      0.12302495     0.005783623  
+      1800         100   0.12902068     0.12902068     0.08608601     0.0019792233 
+      1900         100   0.080857094    0.080857094    0.059672509    0.0022973108 
+      2000         100   0.064403955    0.064403955    0.046429731    0.0011922926 
+      2100         100   0.056475498    0.056475498    0.038678923    0.00085304992
+      2200         100   0.050018256    0.050018256    0.034384821    0.0032112539 
+      2300         100   0.021868304    0.021868304    0.017658151    0.0011526373 
+      2400         100   0.022189236    0.022189236    0.016714436    0.00056488482
+      2500         100   0.012569738    0.012569738    0.010200523    0.00061305414
+      2600         100   0.010861951    0.010861951    0.0086986505   0.00028075976
+      2700         100   0.0092647871   0.0092647871   0.0071124847   0.00043064637
+      2800         100   0.0078527688   0.0078527688   0.0059155703   0.00016902461
+      2900         100   0.0048376734   0.0048376734   0.0039864566   9.6898167e-05
+      3000         100   0.004997394    0.004997394    0.0038195379   0.00012912771
+      3100         100   0.0025381263   0.0025381263   0.0022290621   9.3139494e-05
+      3200         100   0.0023614621   0.0023614621   0.0020627353   0.00043394794
+      3300         100   0.0018926758   0.0018926758   0.0016726508   9.015816e-05 
+      3400         100   0.0016956727   0.0016956727   0.0015060379   9.8437955e-05
+      3500         100   0.0020822011   0.0020822011   0.0016148425   6.8104893e-05
+      3600         100   0.0010660921   0.0010660921   0.0010106443  -4.0921854e-05
+      3700         100   0.00093117128  0.00093117128  0.00086120243  3.9299397e-05
+      3800         100   0.00083426775  0.00083426775  0.00075721786  3.2376e-05   
+      3900         100   0.00076790351  0.00076790351  0.00070733354  3.2793518e-05
+      4000         100   0.0006859536   0.0006859536   0.00062258677  3.0547763e-05
+      4100         100   0.00050291116  0.00050291116  0.00047200581  0.00015040263
+      4200         100   0.00038735513  0.00038735513  0.0003849192   0.00017016843
+      4300         100   0.00031672623  0.00031672623  0.00032789248  7.1880229e-05
+      4400         100   0.00027595545  0.00027595545  0.00029274116  3.120052e-05 
+      4500         100   0.00027092394  0.00027092394  0.00028257706  4.1409733e-05
+      4600         100   0.00026641048  0.00026641048  0.00027631265  3.2258687e-05
+      4700         100   0.0002550395   0.0002550395   0.00026456068  4.4752996e-05
+      4800         100   0.00023866037  0.00023866037  0.00025120225  3.3651155e-05
+      4900         100   0.00019734428  0.00019734428  0.0002099377   2.7700004e-05
+      5000         100   0.00019733184  0.00019733184  0.00020831062  2.6903281e-05
+Loop time of 0.377792 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5717435.568 tau/day, 13234.805 timesteps/s, 1.323 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    | 0.0034096  | 0.0034096  | 0.0034096  |   0.0 |  0.90
+Neigh   | 0.0046279  | 0.0046279  | 0.0046279  |   0.0 |  1.22
+Comm    | 0.00036326 | 0.00036326 | 0.00036326 |   0.0 |  0.10
+Output  | 0.31831    | 0.31831    | 0.31831    |   0.0 | 84.25
+Modify  | 0.049948   | 0.049948   | 0.049948   |   0.0 | 13.22
+Other   |            | 0.001137   |            |       |  0.30
+
+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:            160 ave         160 max         160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 160
+Ave neighs/atom = 1.6
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00019733184  0.00019733184  0.00020831062  2.6930089e-05
+      5100         100   0.14755911     0.14755911     0.085321575    0.0037275005 
+      5200         100   0.17345004     0.17345004     0.10013131     0.0029005613 
+      5300         100   0.17839393     0.17839393     0.09955336     0.0024744353 
+      5400         100   0.18892743     0.18892743     0.10178919     0.0032939874 
+      5500         100   0.19613791     0.19613791     0.10380256     0.0027253339 
+      5600         100   0.19978293     0.19978293     0.10442183     0.0031193701 
+      5700         100   0.21239814     0.21239814     0.10965684     0.0027404998 
+      5800         100   0.22432265     0.22432265     0.11476437     0.0031430877 
+      5900         100   0.22942225     0.22942225     0.11733388     0.00357628   
+      6000         100   0.24043354     0.24043354     0.12272731     0.003255827  
+      6100         100   0.25159401     0.25159401     0.1279307      0.0040378705 
+      6200         100   0.25902708     0.25902708     0.13158752     0.0036512959 
+      6300         100   0.2659723      0.2659723      0.13535001     0.0037298324 
+      6400         100   0.27607055     0.27607055     0.14001655     0.0043863861 
+      6500         100   0.28259585     0.28259585     0.14337861     0.004432214  
+      6600         100   0.29041535     0.29041535     0.14658628     0.0041374757 
+      6700         100   0.29338383     0.29338383     0.14816762     0.0043726723 
+      6800         100   0.29363497     0.29363497     0.14803605     0.0048496941 
+      6900         100   0.29819446     0.29819446     0.14992058     0.0048661826 
+      7000         100   0.30253288     0.30253288     0.15178707     0.0047893404 
+      7100         100   0.30364521     0.30364521     0.15238027     0.0053735204 
+      7200         100   0.30571022     0.30571022     0.15341639     0.0050547621 
+      7300         100   0.30762729     0.30762729     0.15433251     0.0048579985 
+      7400         100   0.30739457     0.30739457     0.15429161     0.0052840169 
+      7500         100   0.3095106      0.3095106      0.15546551     0.0047742904 
+      7600         100   0.30994994     0.30994994     0.15560402     0.0055289317 
+      7700         100   0.3102136      0.3102136      0.1555494      0.0053911148 
+      7800         100   0.31109652     0.31109652     0.15598755     0.0050957646 
+      7900         100   0.31190144     0.31190144     0.15640137     0.0050144069 
+      8000         100   0.3124433      0.3124433      0.15676067     0.0049291948 
+      8100         100   0.31255831     0.31255831     0.15682783     0.0053772662 
+      8200         100   0.31276764     0.31276764     0.15700445     0.0051137616 
+      8300         100   0.31476621     0.31476621     0.15777763     0.0050115786 
+      8400         100   0.31520108     0.31520108     0.1579466      0.0052663181 
+      8500         100   0.31519638     0.31519638     0.15797839     0.0054592691 
+      8600         100   0.31650736     0.31650736     0.15853548     0.006061159  
+      8700         100   0.31783185     0.31783185     0.15910269     0.0055642729 
+      8800         100   0.31962922     0.31962922     0.15981552     0.0051073677 
+      8900         100   0.32028059     0.32028059     0.16016593     0.0051129724 
+      9000         100   0.32067355     0.32067355     0.16033852     0.005334504  
+      9100         100   0.32073134     0.32073134     0.16036476     0.0052193698 
+      9200         100   0.32149618     0.32149618     0.16073834     0.0051959338 
+      9300         100   0.32200413     0.32200413     0.16101431     0.0053371119 
+      9400         100   0.32243427     0.32243427     0.16127313     0.0051442587 
+      9500         100   0.32287887     0.32287887     0.16159452     0.0051133998 
+      9600         100   0.32358279     0.32358279     0.16193072     0.0051698096 
+      9700         100   0.32486591     0.32486591     0.16249108     0.0052421695 
+      9800         100   0.32481094     0.32481094     0.16244971     0.0052881334 
+      9900         100   0.32619742     0.32619742     0.16300857     0.0056091381 
+     10000         100   0.32685101     0.32685101     0.16333907     0.0052565109 
+Loop time of 0.395516 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5461219.023 tau/day, 12641.711 timesteps/s, 1.264 Matom-step/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0097241  | 0.0097241  | 0.0097241  |   0.0 |  2.46
+Neigh   | 0.0063725  | 0.0063725  | 0.0063725  |   0.0 |  1.61
+Comm    | 0.00038378 | 0.00038378 | 0.00038378 |   0.0 |  0.10
+Output  | 0.31516    | 0.31516    | 0.31516    |   0.0 | 79.68
+Modify  | 0.062652   | 0.062652   | 0.062652   |   0.0 | 15.84
+Other   |            | 0.001224   |            |       |  0.31
+
+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:            190 ave         190 max         190 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 190
+Ave neighs/atom = 1.9
+Neighbor list builds = 334
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   0.32685101     0.32685101     0.16333907     0.0052114688 
+     10100         100   0.082150677    0.082150677    0.051495507    0.0065164512 
+     10200         100   0.044140364    0.044140364    0.034724328    0.0010465239 
+     10300         100   0.033122648    0.033122648    0.026625827    0.0022974917 
+     10400         100   0.026649705    0.026649705    0.021846707    0.00035032509
+     10500         100   0.022611369    0.022611369    0.018405546    0.0004069116 
+     10600         100   0.018296124    0.018296124    0.014829351    0.00026270833
+     10700         100   0.015248747    0.015248747    0.012084705    0.00023227455
+     10800         100   0.014989372    0.014989372    0.011849067    0.00054473331
+     10900         100   0.011865503    0.011865503    0.0094526639   0.00028431427
+     11000         100   0.0096206477   0.0096206477   0.0077795159   0.00012996686
+     11100         100   0.0085270379   0.0085270379   0.0069458369   0.00021692214
+     11200         100   0.00760939     0.00760939     0.0062336019   0.00015816658
+     11300         100   0.0070094711   0.0070094711   0.0056987409   9.7160075e-05
+     11400         100   0.0064681327   0.0064681327   0.0053334513   0.0001693687 
+     11500         100   0.0054400476   0.0054400476   0.0044705267   8.1382559e-05
+     11600         100   0.005206949    0.005206949    0.0042892806   7.0309283e-05
+     11700         100   0.0044637648   0.0044637648   0.0037251717   5.4172517e-05
+     11800         100   0.0039969168   0.0039969168   0.003362444    2.0226315e-05
+     11900         100   0.0033117132   0.0033117132   0.0027762101   5.2311253e-05
+     12000         100   0.0031073405   0.0031073405   0.0025984799   3.9890528e-05
+     12100         100   0.0029847617   0.0029847617   0.0025070771  -5.7259344e-06
+     12200         100   0.0028458878   0.0028458878   0.0024108535   3.5217862e-05
+     12300         100   0.0026501923   0.0026501923   0.0022711794   0.00012033569
+     12400         100   0.0025425504   0.0025425504   0.0021847643   3.1464061e-05
+     12500         100   0.0024161319   0.0024161319   0.0020843813   0.00014941327
+     12600         100   0.002341327    0.002341327    0.0020232445   2.8973921e-05
+     12700         100   0.0022334192   0.0022334192   0.0019425572   3.0790164e-05
+     12800         100   0.0021889403   0.0021889403   0.0019088353   2.9638662e-05
+     12900         100   0.0020442842   0.0020442842   0.0018049012   2.5298016e-05
+     13000         100   0.001803154    0.001803154    0.0016328702   2.2314031e-05
+     13100         100   0.0016791405   0.0016791405   0.0015327583   2.2967562e-05
+     13200         100   0.001622137    0.001622137    0.0014810169   4.0326561e-05
+     13300         100   0.001601531    0.001601531    0.0014650816   1.9818946e-05
+     13400         100   0.0015591399   0.0015591399   0.0014123726   2.119773e-05 
+     13500         100   0.0014546357   0.0014546357   0.0013328423   1.8001117e-05
+     13600         100   0.0013998773   0.0013998773   0.0012913696   2.6202181e-05
+     13700         100   0.001367574    0.001367574    0.0012631494   1.6923729e-05
+     13800         100   0.001225732    0.001225732    0.0011125165   1.4445147e-05
+     13900         100   0.0012086291   0.0012086291   0.0010972374   2.8597468e-05
+     14000         100   0.0011916306   0.0011916306   0.0010833978   7.2381933e-05
+     14100         100   0.0011461149   0.0011461149   0.0010110271   1.4183172e-05
+     14200         100   0.0011209785   0.0011209785   0.00099190436  1.1546608e-05
+     14300         100   0.0011050802   0.0011050802   0.00098070422  1.3675367e-05
+     14400         100   0.0010910417   0.0010910417   0.00097025303  1.3501641e-05
+     14500         100   0.0010645152   0.0010645152   0.00093785696  1.3173375e-05
+     14600         100   0.0010479185   0.0010479185   0.00092353031  2.5164629e-05
+     14700         100   0.00099034477  0.00099034477  0.0008638973   1.2874356e-05
+     14800         100   0.00099115544  0.00099115544  0.00086195396  1.2265549e-05
+     14900         100   0.00097510619  0.00097510619  0.00083043649  6.0289327e-05
+     15000         100   0.00095883902  0.00095883902  0.00080522184  1.1865633e-05
+Loop time of 0.389832 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5540855.231 tau/day, 12826.054 timesteps/s, 1.283 Matom-step/s
+96.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0031065  | 0.0031065  | 0.0031065  |   0.0 |  0.80
+Neigh   | 0.0014317  | 0.0014317  | 0.0014317  |   0.0 |  0.37
+Comm    | 0.000314   | 0.000314   | 0.000314   |   0.0 |  0.08
+Output  | 0.32805    | 0.32805    | 0.32805    |   0.0 | 84.15
+Modify  | 0.055756   | 0.055756   | 0.055756   |   0.0 | 14.30
+Other   |            | 0.001173   |            |       |  0.30
+
+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:            165 ave         165 max         165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 165
+Ave neighs/atom = 1.65
+Neighbor list builds = 69
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00095883902  0.00095883902  0.00080522184  1.1865633e-05
+     15100         100   0.16225441     0.16225441     0.098498099    0.0064159333 
+     15200         100   0.22482098     0.22482098     0.12948232     0.003576331  
+     15300         100   0.2458026      0.2458026      0.1393646      0.006749306  
+     15400         100   0.26239222     0.26239222     0.1469859      0.0089800228 
+     15500         100   0.28687382     0.28687382     0.15847135     0.0079704333 
+     15600         100   0.28622953     0.28622953     0.15902139     0.0082281462 
+     15700         100   0.30668089     0.30668089     0.16265483     0.014688893  
+     15800         100   0.33007713     0.33007713     0.17247344     0.0099574571 
+     15900         100   0.35773029     0.35773029     0.18298391     0.01415523   
+     16000         100   0.36309971     0.36309971     0.18514042     0.010763173  
+     16100         100   0.36974105     0.36974105     0.18746237     0.010738235  
+     16200         100   0.36988383     0.36988383     0.18775314     0.014768427  
+     16300         100   0.37560588     0.37560588     0.19010652     0.014297415  
+     16400         100   0.37747146     0.37747146     0.19143031     0.014086853  
+     16500         100   0.38053331     0.38053331     0.19248441     0.01837541   
+     16600         100   0.37315821     0.37315821     0.1881627      0.0098076132 
+     16700         100   0.38286964     0.38286964     0.19289589     0.011785316  
+     16800         100   0.38013501     0.38013501     0.19200912     0.0138546    
+     16900         100   0.37496008     0.37496008     0.19035729     0.010235176  
+     17000         100   0.365244       0.365244       0.18508129     0.011814705  
+     17100         100   0.36324363     0.36324363     0.18539176     0.0077602876 
+     17200         100   0.36563128     0.36563128     0.18828717     0.009760622  
+     17300         100   0.41040797     0.41040797     0.21297576     0.0060030421 
+     17400         100   0.42784496     0.42784496     0.22357917     0.0072328321 
+     17500         100   0.44480315     0.44480315     0.23296103     0.0081208771 
+     17600         100   0.49540498     0.49540498     0.26207461     0.0094193362 
+     17700         100   0.53563972     0.53563972     0.28429788     0.0096153439 
+     17800         100   0.59909402     0.59909402     0.31832665     0.0086897236 
+     17900         100   0.65975736     0.65975736     0.35361646     0.010946403  
+     18000         100   0.67883738     0.67883738     0.36868438     0.010453697  
+     18100         100   0.67229859     0.67229859     0.37009573     0.011447688  
+     18200         100   0.58740281     0.58740281     0.32918911     0.012430038  
+     18300         100   0.51321184     0.51321184     0.29212329     0.014782894  
+     18400         100   0.46432678     0.46432678     0.26861208     0.0074401518 
+     18500         100   0.46083979     0.46083979     0.26638884     0.0090587319 
+     18600         100   0.41968764     0.41968764     0.24616432     0.0091476182 
+     18700         100   0.40749768     0.40749768     0.24073731     0.0073954099 
+     18800         100   0.38490007     0.38490007     0.23057035     0.0056617504 
+     18900         100   0.36115679     0.36115679     0.21996888     0.0069095868 
+     19000         100   0.31118149     0.31118149     0.19549915     0.0066423887 
+     19100         100   0.34419249     0.34419249     0.20736311     0.012418102  
+     19200         100   0.33174248     0.33174248     0.19629654     0.0074405926 
+     19300         100   0.33028394     0.33028394     0.19472996     0.0077286569 
+     19400         100   0.33612501     0.33612501     0.19522775     0.0083424841 
+     19500         100   0.32216161     0.32216161     0.18401278     0.0088692814 
+     19600         100   0.33681829     0.33681829     0.18758804     0.0097379383 
+     19700         100   0.33730835     0.33730835     0.18474995     0.009296681  
+     19800         100   0.3351213      0.3351213      0.18164387     0.0061672199 
+     19900         100   0.32674396     0.32674396     0.17780137     0.0062277401 
+     20000         100   0.31549601     0.31549601     0.17276762     0.011954545  
+Loop time of 0.416473 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5186412.038 tau/day, 12005.583 timesteps/s, 1.201 Matom-step/s
+95.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0092038  | 0.0092038  | 0.0092038  |   0.0 |  2.21
+Neigh   | 0.0099854  | 0.0099854  | 0.0099854  |   0.0 |  2.40
+Comm    | 0.00041171 | 0.00041171 | 0.00041171 |   0.0 |  0.10
+Output  | 0.33871    | 0.33871    | 0.33871    |   0.0 | 81.33
+Modify  | 0.056911   | 0.056911   | 0.056911   |   0.0 | 13.67
+Other   |            | 0.001256   |            |       |  0.30
+
+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:            242 ave         242 max         242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 242
+Ave neighs/atom = 2.42
+Neighbor list builds = 435
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   0.31549601     0.31549601     0.17276762     0.011924862  
+     20100         100   0.067243668    0.067243668    0.051058315    0.0026847669 
+     20200         100   0.064954648    0.064954648    0.04577406     0.0031985925 
+     20300         100   0.081722159    0.081722159    0.052328099    0.003382093  
+     20400         100   0.052538018    0.052538018    0.038041695    0.0080953559 
+     20500         100   0.045138106    0.045138106    0.032227169    0.0035839274 
+     20600         100   0.044187088    0.044187088    0.031849801    0.0032417719 
+     20700         100   0.048791318    0.048791318    0.033838035    0.0030783015 
+     20800         100   0.042228029    0.042228029    0.029496426    0.0026771471 
+     20900         100   0.037884649    0.037884649    0.026659395    0.0016131444 
+     21000         100   0.036121934    0.036121934    0.025961479    0.0033546991 
+     21100         100   0.041151215    0.041151215    0.028554924    0.0014986709 
+     21200         100   0.032352882    0.032352882    0.024166876    0.0018674452 
+     21300         100   0.033808076    0.033808076    0.02501534     0.0014150028 
+     21400         100   0.033233201    0.033233201    0.024762604    0.0015124318 
+     21500         100   0.023344798    0.023344798    0.017595957    0.0020406313 
+     21600         100   0.024137168    0.024137168    0.017835056    0.001648494  
+     21700         100   0.020201901    0.020201901    0.015367789    0.0014089977 
+     21800         100   0.019279358    0.019279358    0.014625498    0.0012643094 
+     21900         100   0.01893081     0.01893081     0.014292746    0.0015049479 
+     22000         100   0.017257227    0.017257227    0.01315079     0.0011652685 
+     22100         100   0.015479952    0.015479952    0.011715026    0.0014536538 
+     22200         100   0.016610168    0.016610168    0.012253776    0.00089466949
+     22300         100   0.014924039    0.014924039    0.011273468    0.0010494839 
+     22400         100   0.015991668    0.015991668    0.011902404    0.00082344174
+     22500         100   0.011574074    0.011574074    0.0087681303   0.00081009385
+     22600         100   0.012494171    0.012494171    0.0092328529   0.0005622816 
+     22700         100   0.011070984    0.011070984    0.0083661745   0.00080065357
+     22800         100   0.01131513     0.01131513     0.0084259241   0.00073680805
+     22900         100   0.010217077    0.010217077    0.0077647566   0.00053727888
+     23000         100   0.0099409381   0.0099409381   0.0074288509   0.00058448502
+     23100         100   0.0091176585   0.0091176585   0.0069209665   0.00063336231
+     23200         100   0.0083540727   0.0083540727   0.0063805491   0.0005281495 
+     23300         100   0.008619666    0.008619666    0.0065404908   0.0005398125 
+     23400         100   0.0088762213   0.0088762213   0.0065206851   0.00046304022
+     23500         100   0.007364061    0.007364061    0.0055771232   0.00046541178
+     23600         100   0.0074046272   0.0074046272   0.0055598275   0.00036522805
+     23700         100   0.0073881556   0.0073881556   0.0055580858   0.0005353812 
+     23800         100   0.0072954594   0.0072954594   0.0053965497   0.00041955961
+     23900         100   0.006566226    0.006566226    0.0047704154   0.00037213632
+     24000         100   0.0052279617   0.0052279617   0.0039151171   0.00039220479
+     24100         100   0.004661037    0.004661037    0.0035353607   0.00036592087
+     24200         100   0.0046822639   0.0046822639   0.0035561511   0.00036233017
+     24300         100   0.0047878887   0.0047878887   0.0036222045   0.0003906286 
+     24400         100   0.005705559    0.005705559    0.0041298188   0.00039793154
+     24500         100   0.0038440196   0.0038440196   0.0030815263   0.00050064408
+     24600         100   0.0035754817   0.0035754817   0.0030293001   0.00032292161
+     24700         100   0.003446554    0.003446554    0.0027976688   0.00029115924
+     24800         100   0.0028987207   0.0028987207   0.0023988341   0.00018959598
+     24900         100   0.0027083267   0.0027083267   0.0021669208   0.0001799362 
+     25000         100   0.0026561456   0.0026561456   0.0020638865   0.00014386648
+Loop time of 0.394353 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5477329.555 tau/day, 12679.004 timesteps/s, 1.268 Matom-step/s
+82.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0073102  | 0.0073102  | 0.0073102  |   0.0 |  1.85
+Neigh   | 0.00398    | 0.00398    | 0.00398    |   0.0 |  1.01
+Comm    | 0.00033952 | 0.00033952 | 0.00033952 |   0.0 |  0.09
+Output  | 0.32686    | 0.32686    | 0.32686    |   0.0 | 82.89
+Modify  | 0.054687   | 0.054687   | 0.054687   |   0.0 | 13.87
+Other   |            | 0.001176   |            |       |  0.30
+
+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:            147 ave         147 max         147 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 147
+Ave neighs/atom = 1.47
+Neighbor list builds = 173
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/gransurf/log.1Jul24.tribox.gran.global.g++.4

@@ -0,0 +1,492 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+molecule        tris surf.tribox
+Read molecule template tris:
+LAMMPS data file for tri box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  24 triangles with 14 points
+
+fix             20 all surface/global tris hooke                 4000.0 NULL 100.0 NULL 0.5 1
+#fix             20 all surface/global tris hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 1 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 yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.4855 | 0.4855 | 0.4855 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       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   0.82347039     0.82347039     0.41172861     0.0029850802 
+       500          30   0.76963938     0.76963938     0.38709352     0.0042867255 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          64   0.51325196     0.51325196     0.26472957     0.0045780407 
+       700          64   0.57133229     0.57133229     0.29476966     0.0046847812 
+       800          64   0.630634       0.630634       0.32751956     0.0050038133 
+       900          64   0.54233611     0.54233611     0.28819808     0.0052880896 
+      1000          64   0.48543152     0.48543152     0.26491902     0.0064773948 
+      1100          64   0.47303609     0.47303609     0.2578388      0.0057125611 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          99   0.40053109     0.40053109     0.2195167      0.0081778049 
+      1300          99   0.42696772     0.42696772     0.23049402     0.006385146  
+      1400          99   0.37139574     0.37139574     0.20331799     0.0074485306 
+      1500          99   0.33478846     0.33478846     0.18670496     0.0061673941 
+      1600          99   0.29982872     0.29982872     0.16693769     0.0051747984 
+      1700         100   0.2069625      0.2069625      0.12302495     0.005783624  
+      1800         100   0.12902068     0.12902068     0.08608601     0.0019792234 
+      1900         100   0.080857095    0.080857095    0.05967251     0.0022973101 
+      2000         100   0.064403959    0.064403959    0.046429734    0.0011922946 
+      2100         100   0.056475466    0.056475466    0.038678907    0.00085302928
+      2200         100   0.050018273    0.050018273    0.03438483     0.0032112547 
+      2300         100   0.02186833     0.02186833     0.01765815     0.001152603  
+      2400         100   0.02218925     0.02218925     0.016714386    0.00056474678
+      2500         100   0.012569988    0.012569988    0.010200648    0.0006133907 
+      2600         100   0.010862479    0.010862479    0.0086989172   0.00028072722
+      2700         100   0.0092737903   0.0092737903   0.0071165383   0.00041430278
+      2800         100   0.0078587709   0.0078587709   0.00592121     0.00017374958
+      2900         100   0.0048613617   0.0048613617   0.004000904    0.00021321956
+      3000         100   0.0050147313   0.0050147313   0.0038322501   0.00017831675
+      3100         100   0.0025550411   0.0025550411   0.0022405824   6.8592843e-05
+      3200         100   0.0023577912   0.0023577912   0.0020418633   0.0003584618 
+      3300         100   0.0018996206   0.0018996206   0.0016777567   7.5165222e-05
+      3400         100   0.001694751    0.001694751    0.0015042348   0.00014566717
+      3500         100   0.0020882068   0.0020882068   0.0016170458   8.7027542e-05
+      3600         100   0.0010813667   0.0010813667   0.0010137349   8.5126382e-05
+      3700         100   0.00094548982  0.00094548982  0.00086966169  4.2409893e-05
+      3800         100   0.00084816181  0.00084816181  0.00077098131  3.011429e-05 
+      3900         100   0.00078382097  0.00078382097  0.00071960486  5.939333e-05 
+      4000         100   0.00075302926  0.00075302926  0.00067851822  3.2758594e-05
+      4100         100   0.00051405526  0.00051405526  0.00048629367  0.00013859285
+      4200         100   0.00038825626  0.00038825626  0.00038868575  0.00020599691
+      4300         100   0.00031919597  0.00031919597  0.00033058576  0.00010854923
+      4400         100   0.00029919941  0.00029919941  0.00031222783  7.2391663e-05
+      4500         100   0.0002903216   0.0002903216   0.00029974662  5.5125563e-05
+      4600         100   0.0002753977   0.0002753977   0.00028258456  9.6552286e-05
+      4700         100   0.00027064725  0.00027064725  0.0002776974   4.0309048e-05
+      4800         100   0.00024203571  0.00024203571  0.00025112727  3.3700422e-05
+      4900         100   0.00020539914  0.00020539914  0.00021705763  2.7873051e-05
+      5000         100   0.00018816565  0.00018816565  0.00020135634  4.7752851e-05
+Loop time of 0.63402 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3406832.319 tau/day, 7886.186 timesteps/s, 788.619 katom-step/s
+95.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00025776 | 0.0013928  | 0.002766   |   3.1 |  0.22
+Neigh   | 0.0012616  | 0.0021326  | 0.002909   |   1.4 |  0.34
+Comm    | 0.0072148  | 0.011698   | 0.016249   |   4.0 |  1.85
+Output  | 0.41173    | 0.47818    | 0.57141    |   9.8 | 75.42
+Modify  | 0.0023688  | 0.01821    | 0.036988   |  11.8 |  2.87
+Other   |            | 0.1224     |            |       | 19.31
+
+Nlocal:             25 ave          50 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            4.5 ave           9 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           40.5 ave          82 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 162
+Ave neighs/atom = 1.62
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.548 | 4.611 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00018816565  0.00018816565  0.00020135634  4.4246792e-05
+      5100         100   0.14937779     0.14937779     0.086114773    0.0025984359 
+      5200         100   0.17697193     0.17697193     0.1019691      0.0026173891 
+      5300         100   0.18255024     0.18255024     0.10122134     0.0041759269 
+      5400         100   0.19510207     0.19510207     0.1050284      0.0027541295 
+      5500         100   0.1980801      0.1980801      0.10458743     0.0027957101 
+      5600         100   0.20490362     0.20490362     0.10674522     0.002985542  
+      5700         100   0.21087885     0.21087885     0.10861062     0.0030935481 
+      5800         100   0.22309411     0.22309411     0.11419601     0.0029760547 
+      5900         100   0.22880189     0.22880189     0.1171042      0.0029681474 
+      6000         100   0.2363739      0.2363739      0.12083453     0.0032437464 
+      6100         100   0.24581768     0.24581768     0.12531649     0.0032571271 
+      6200         100   0.25161424     0.25161424     0.12838601     0.0034995369 
+      6300         100   0.25972194     0.25972194     0.13241738     0.0035882457 
+      6400         100   0.2678312      0.2678312      0.13632033     0.0036612131 
+      6500         100   0.27990358     0.27990358     0.14189324     0.0046486676 
+      6600         100   0.2827759      0.2827759      0.14317296     0.0048164853 
+      6700         100   0.2897351      0.2897351      0.14616568     0.0042753049 
+      6800         100   0.29164978     0.29164978     0.14688678     0.0040397004 
+      6900         100   0.29377421     0.29377421     0.14786359     0.0051561937 
+      7000         100   0.29698841     0.29698841     0.14947643     0.0046008044 
+      7100         100   0.3019081      0.3019081      0.15147175     0.0065696769 
+      7200         100   0.30532028     0.30532028     0.1531023      0.0045987829 
+      7300         100   0.30629289     0.30629289     0.15368598     0.0048558556 
+      7400         100   0.30534641     0.30534641     0.15316839     0.0057637671 
+      7500         100   0.30786877     0.30786877     0.15429461     0.004843753  
+      7600         100   0.30862009     0.30862009     0.15464621     0.0052118056 
+      7700         100   0.30900657     0.30900657     0.15478242     0.0048879932 
+      7800         100   0.31054034     0.31054034     0.1554636      0.0052082034 
+      7900         100   0.31174887     0.31174887     0.15610325     0.0049178073 
+      8000         100   0.31247071     0.31247071     0.15647921     0.0052603626 
+      8100         100   0.31273024     0.31273024     0.15659099     0.0056001647 
+      8200         100   0.3140235      0.3140235      0.15727592     0.004977821  
+      8300         100   0.31383701     0.31383701     0.15715969     0.0052231004 
+      8400         100   0.31509644     0.31509644     0.15775385     0.0050051889 
+      8500         100   0.31498521     0.31498521     0.15762151     0.0052864908 
+      8600         100   0.31575201     0.31575201     0.15792624     0.0050759547 
+      8700         100   0.31620758     0.31620758     0.15818292     0.0050530619 
+      8800         100   0.31691036     0.31691036     0.15860213     0.005004857  
+      8900         100   0.31659627     0.31659627     0.15846212     0.0050695163 
+      9000         100   0.31769151     0.31769151     0.15903638     0.0050507355 
+      9100         100   0.31716143     0.31716143     0.15881355     0.005017094  
+      9200         100   0.31633956     0.31633956     0.1585031      0.0053446628 
+      9300         100   0.31655443     0.31655443     0.15863537     0.0049328007 
+      9400         100   0.31599503     0.31599503     0.15822485     0.0049933297 
+      9500         100   0.31660281     0.31660281     0.15853731     0.0049387958 
+      9600         100   0.31664518     0.31664518     0.15861539     0.0049222414 
+      9700         100   0.31824803     0.31824803     0.15934333     0.0052873464 
+      9800         100   0.31820192     0.31820192     0.15932994     0.0049687062 
+      9900         100   0.31846082     0.31846082     0.15943054     0.0053817995 
+     10000         100   0.31969811     0.31969811     0.15997735     0.005012462  
+Loop time of 0.547282 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3946778.087 tau/day, 9136.060 timesteps/s, 913.606 katom-step/s
+97.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00017514 | 0.0033369  | 0.0067434  |   5.4 |  0.61
+Neigh   | 0.0011683  | 0.0026653  | 0.003952   |   2.5 |  0.49
+Comm    | 0.0061274  | 0.010042   | 0.013959   |   3.9 |  1.83
+Output  | 0.36944    | 0.41287    | 0.47628    |   6.7 | 75.44
+Modify  | 0.0022896  | 0.021864   | 0.042571   |  13.2 |  4.00
+Other   |            | 0.0965     |            |       | 17.63
+
+Nlocal:             25 ave          52 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4.25 ave           9 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:           47.5 ave         111 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 190
+Ave neighs/atom = 1.9
+Neighbor list builds = 334
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.548 | 4.611 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   0.31969811     0.31969811     0.15997735     0.005039886  
+     10100         100   0.096856693    0.096856693    0.061256799    0.0017653508 
+     10200         100   0.06374563     0.06374563     0.049164989    0.00074375479
+     10300         100   0.053346958    0.053346958    0.041648676    0.00088021828
+     10400         100   0.04530167     0.04530167     0.035468031    0.0006357307 
+     10500         100   0.036511473    0.036511473    0.02864095     0.00046569718
+     10600         100   0.031850796    0.031850796    0.024752197    0.001484525  
+     10700         100   0.027853481    0.027853481    0.021856016    0.00083233598
+     10800         100   0.023988298    0.023988298    0.018551491    0.00025321878
+     10900         100   0.022362927    0.022362927    0.01775739     0.00027674123
+     11000         100   0.019598739    0.019598739    0.01566657     0.00029114873
+     11100         100   0.016949467    0.016949467    0.013323455    0.00054759179
+     11200         100   0.013201141    0.013201141    0.010205793    0.00046859829
+     11300         100   0.010724903    0.010724903    0.0083548813   0.00016110668
+     11400         100   0.0094528501   0.0094528501   0.0074254702   0.00012282294
+     11500         100   0.0081681904   0.0081681904   0.0064435379   0.00018389596
+     11600         100   0.0080112061   0.0080112061   0.006319339    9.9138675e-05
+     11700         100   0.0072316886   0.0072316886   0.0056968863   8.9492146e-05
+     11800         100   0.0066741475   0.0066741475   0.0052653282   9.1792343e-05
+     11900         100   0.0060596979   0.0060596979   0.0048019244   0.00059435717
+     12000         100   0.0058193298   0.0058193298   0.0046098949   7.2231759e-05
+     12100         100   0.0053847114   0.0053847114   0.0042545862   9.3394135e-05
+     12200         100   0.0049412476   0.0049412476   0.0039106158   0.00010078502
+     12300         100   0.004572105    0.004572105    0.0036504695   5.5867397e-05
+     12400         100   0.0042412045   0.0042412045   0.0034175496   0.00036582163
+     12500         100   0.0035923846   0.0035923846   0.0029316243   6.9114212e-05
+     12600         100   0.0032446947   0.0032446947   0.0026668677   4.1659699e-05
+     12700         100   0.003132735    0.003132735    0.0025875973   5.6802791e-05
+     12800         100   0.0030486242   0.0030486242   0.0025160882   0.00024777199
+     12900         100   0.0029017497   0.0029017497   0.0024179283   6.7491687e-05
+     13000         100   0.0027960043   0.0027960043   0.0023415783   3.4600553e-05
+     13100         100   0.0024698607   0.0024698607   0.0020868913   0.00015330841
+     13200         100   0.0023835355   0.0023835355   0.0020283653   2.9496252e-05
+     13300         100   0.0021088439   0.0021088439   0.0018016867   5.3026287e-05
+     13400         100   0.0018955838   0.0018955838   0.0016251265   5.6464898e-05
+     13500         100   0.0017787595   0.0017787595   0.0015273835   0.00010533321
+     13600         100   0.0017398053   0.0017398053   0.0015003761   2.153009e-05 
+     13700         100   0.0017070216   0.0017070216   0.0014780376   2.2369503e-05
+     13800         100   0.0016227474   0.0016227474   0.0014210693   6.9106097e-05
+     13900         100   0.0016020414   0.0016020414   0.0013971016   1.9825262e-05
+     14000         100   0.0015849364   0.0015849364   0.0013841731   1.9613588e-05
+     14100         100   0.0014802906   0.0014802906   0.001301188    2.3602632e-05
+     14200         100   0.0014452784   0.0014452784   0.0012723611   5.4930779e-05
+     14300         100   0.0013373933   0.0013373933   0.0011970238   7.7331197e-05
+     14400         100   0.0012644873   0.0012644873   0.0011371743   3.3804604e-05
+     14500         100   0.0012269172   0.0012269172   0.0011090464   0.00019066733
+     14600         100   0.0011790378   0.0011790378   0.0010710915   2.2152438e-05
+     14700         100   0.001141029    0.001141029    0.0010389261   1.4725855e-05
+     14800         100   0.001136936    0.001136936    0.0010350762   1.833013e-05 
+     14900         100   0.0010587639   0.0010587639   0.00097375352  1.3102203e-05
+     15000         100   0.0010255325   0.0010255325   0.00094590806  1.5126454e-05
+Loop time of 0.580448 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3721260.712 tau/day, 8614.029 timesteps/s, 861.403 katom-step/s
+97.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00018589 | 0.0012662  | 0.0025061  |   3.1 |  0.22
+Neigh   | 0.00039462 | 0.00072277 | 0.0010682  |   0.0 |  0.12
+Comm    | 0.0012803  | 0.0072067  | 0.013189   |   7.0 |  1.24
+Output  | 0.39942    | 0.45124    | 0.51979    |   6.9 | 77.74
+Modify  | 0.00047645 | 0.019943   | 0.039764   |  13.8 |  3.44
+Other   |            | 0.1001     |            |       | 17.24
+
+Nlocal:             25 ave          50 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4.25 ave          10 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:             37 ave          77 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 148
+Ave neighs/atom = 1.48
+Neighbor list builds = 72
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.548 | 4.611 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.0010255325   0.0010255325   0.00094590806  1.4814045e-05
+     15100         100   0.16111221     0.16111221     0.097982105    0.0056716878 
+     15200         100   0.21347296     0.21347296     0.12567019     0.0029815056 
+     15300         100   0.24705334     0.24705334     0.13884473     0.0078448562 
+     15400         100   0.27522493     0.27522493     0.15035782     0.0073215473 
+     15500         100   0.30348486     0.30348486     0.16433701     0.0068229641 
+     15600         100   0.31550013     0.31550013     0.16857649     0.0077789307 
+     15700         100   0.32318922     0.32318922     0.1719013      0.012280847  
+     15800         100   0.33908701     0.33908701     0.17750923     0.015821994  
+     15900         100   0.35593866     0.35593866     0.18345193     0.021263374  
+     16000         100   0.36889801     0.36889801     0.1869234      0.011456078  
+     16100         100   0.35809835     0.35809835     0.18158992     0.014811103  
+     16200         100   0.36319635     0.36319635     0.18337159     0.012823323  
+     16300         100   0.35852464     0.35852464     0.18081456     0.01280934   
+     16400         100   0.34902631     0.34902631     0.17663396     0.012992629  
+     16500         100   0.33443513     0.33443513     0.16948607     0.012986886  
+     16600         100   0.3150597      0.3150597      0.16079097     0.010586882  
+     16700         100   0.31338609     0.31338609     0.16045733     0.009805616  
+     16800         100   0.30473867     0.30473867     0.15686705     0.014362545  
+     16900         100   0.31270607     0.31270607     0.16119766     0.0070575979 
+     17000         100   0.2832931      0.2832931      0.14785887     0.0039466166 
+     17100         100   0.28215868     0.28215868     0.14795001     0.0068627045 
+     17200         100   0.29701033     0.29701033     0.16099476     0.0040667324 
+     17300         100   0.3665611      0.3665611      0.19664166     0.0065836505 
+     17400         100   0.43400548     0.43400548     0.23335072     0.0096693511 
+     17500         100   0.5057676      0.5057676      0.2773349      0.0071479313 
+     17600         100   0.52614351     0.52614351     0.29090432     0.0095749902 
+     17700         100   0.52478022     0.52478022     0.29525839     0.010528327  
+     17800         100   0.53046479     0.53046479     0.29862674     0.012410569  
+     17900         100   0.51722354     0.51722354     0.29212965     0.0097423802 
+     18000         100   0.51837131     0.51837131     0.29426864     0.010265508  
+     18100         100   0.46407283     0.46407283     0.26786292     0.015842602  
+     18200         100   0.4281392      0.4281392      0.24883206     0.016085526  
+     18300         100   0.36407304     0.36407304     0.22014997     0.0091448904 
+     18400         100   0.32800292     0.32800292     0.20387181     0.0088602724 
+     18500         100   0.30727965     0.30727965     0.18744751     0.0067928429 
+     18600         100   0.31715182     0.31715182     0.19306784     0.0047252497 
+     18700         100   0.29383189     0.29383189     0.18450238     0.0046337396 
+     18800         100   0.28365185     0.28365185     0.1810902      0.005644391  
+     18900         100   0.30670015     0.30670015     0.19521314     0.0048593554 
+     19000         100   0.31681967     0.31681967     0.201889       0.0059511233 
+     19100         100   0.32218287     0.32218287     0.20009306     0.0093378277 
+     19200         100   0.30255724     0.30255724     0.19160821     0.0087838518 
+     19300         100   0.31907942     0.31907942     0.19849225     0.0093802566 
+     19400         100   0.31650176     0.31650176     0.18834128     0.010429547  
+     19500         100   0.32959296     0.32959296     0.19229144     0.012724502  
+     19600         100   0.33134974     0.33134974     0.18581781     0.016960866  
+     19700         100   0.32878109     0.32878109     0.18215506     0.0096165803 
+     19800         100   0.33724696     0.33724696     0.18335211     0.0060443045 
+     19900         100   0.33179464     0.33179464     0.17822307     0.010776083  
+     20000         100   0.34377432     0.34377432     0.1841787      0.0094534745 
+Loop time of 1.31378 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 1644113.102 tau/day, 3805.817 timesteps/s, 380.582 katom-step/s
+96.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0014951  | 0.0059208  | 0.012257   |   5.8 |  0.45
+Neigh   | 0.0055162  | 0.0094303  | 0.017183   |   4.9 |  0.72
+Comm    | 0.051772   | 0.062444   | 0.068614   |   2.5 |  4.75
+Output  | 0.8827     | 0.98488    | 1.1231     |   9.3 | 74.97
+Modify  | 0.02082    | 0.04696    | 0.090098   |  13.2 |  3.57
+Other   |            | 0.2041     |            |       | 15.54
+
+Nlocal:             25 ave          67 max           0 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:           6.25 ave          13 max           0 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:          54.75 ave         156 max           0 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 219
+Ave neighs/atom = 2.19
+Neighbor list builds = 430
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   0.34377432     0.34377432     0.1841787      0.0092764528 
+     20100         100   0.097239014    0.097239014    0.068864895    0.0029157234 
+     20200         100   0.090387219    0.090387219    0.063243792    0.0030276724 
+     20300         100   0.10130213     0.10130213     0.065604495    0.0040954401 
+     20400         100   0.073193003    0.073193003    0.049395297    0.011005746  
+     20500         100   0.064987626    0.064987626    0.042476486    0.0035623578 
+     20600         100   0.056092845    0.056092845    0.035733351    0.0046843988 
+     20700         100   0.047975467    0.047975467    0.031279933    0.006027     
+     20800         100   0.042713655    0.042713655    0.028630415    0.0028623851 
+     20900         100   0.027009619    0.027009619    0.019950334    0.0031930947 
+     21000         100   0.030115735    0.030115735    0.021837467    0.0031118498 
+     21100         100   0.030382146    0.030382146    0.02158358     0.0016950638 
+     21200         100   0.028917881    0.028917881    0.020618558    0.0015449848 
+     21300         100   0.02553423     0.02553423     0.018753907    0.0020401097 
+     21400         100   0.024907599    0.024907599    0.018805009    0.0015219354 
+     21500         100   0.028047498    0.028047498    0.020431592    0.0036172877 
+     21600         100   0.023143766    0.023143766    0.017048059    0.001391321  
+     21700         100   0.025832817    0.025832817    0.018907239    0.0014196777 
+     21800         100   0.02294723     0.02294723     0.016986932    0.00099306999
+     21900         100   0.021774769    0.021774769    0.016357385    0.0015445184 
+     22000         100   0.019488798    0.019488798    0.014411675    0.00096975376
+     22100         100   0.017498173    0.017498173    0.013303102    0.0013869769 
+     22200         100   0.017606431    0.017606431    0.013696534    0.0016275912 
+     22300         100   0.01864478     0.01864478     0.014363082    0.00093199338
+     22400         100   0.017184319    0.017184319    0.013013426    0.0007137204 
+     22500         100   0.016970049    0.016970049    0.012735761    0.00094285653
+     22600         100   0.015601151    0.015601151    0.011558366    0.00064664867
+     22700         100   0.01532704     0.01532704     0.011052585    0.0011443538 
+     22800         100   0.013843117    0.013843117    0.010175224    0.00074058068
+     22900         100   0.0142626      0.0142626      0.010517503    0.00062291367
+     23000         100   0.012672457    0.012672457    0.0095213548   0.00048253765
+     23100         100   0.011770367    0.011770367    0.0088631275   0.0010809683 
+     23200         100   0.0099747299   0.0099747299   0.0076787282   0.00049951509
+     23300         100   0.01031026     0.01031026     0.0079525195   0.00064873732
+     23400         100   0.0096104307   0.0096104307   0.0072783079   0.00045628129
+     23500         100   0.0092403444   0.0092403444   0.0069910691   0.00055860189
+     23600         100   0.0087158451   0.0087158451   0.0064234628   0.00042327506
+     23700         100   0.0076095087   0.0076095087   0.005524052    0.00040612722
+     23800         100   0.0073236191   0.0073236191   0.0054016138   0.0002882358 
+     23900         100   0.0076690517   0.0076690517   0.0054567733   0.000294478  
+     24000         100   0.0068826778   0.0068826778   0.0049332647   0.00025128376
+     24100         100   0.006293019    0.006293019    0.0046682205   0.00029832544
+     24200         100   0.005767467    0.005767467    0.0043594373   0.00026379963
+     24300         100   0.005071854    0.005071854    0.0038348196   0.00026374758
+     24400         100   0.0051487759   0.0051487759   0.0038569741   0.00047689032
+     24500         100   0.0045914722   0.0045914722   0.0034370386   0.00026920355
+     24600         100   0.0042661938   0.0042661938   0.0031638249   0.00023704631
+     24700         100   0.0038978286   0.0038978286   0.0028913869   0.00029112049
+     24800         100   0.0033993745   0.0033993745   0.0025640275   0.00054348397
+     24900         100   0.0030064864   0.0030064864   0.0022631158   0.00016374877
+     25000         100   0.0030540972   0.0030540972   0.0022935172   0.00012379035
+Loop time of 0.686895 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3144587.502 tau/day, 7279.138 timesteps/s, 727.914 katom-step/s
+96.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00021583 | 0.0031591  | 0.0080919  |   5.8 |  0.46
+Neigh   | 0.00087816 | 0.0020995  | 0.0040495  |   2.9 |  0.31
+Comm    | 0.0031121  | 0.011483   | 0.021843   |   7.2 |  1.67
+Output  | 0.45899    | 0.52212    | 0.60018    |   7.4 | 76.01
+Modify  | 0.00065063 | 0.023045   | 0.054608   |  15.4 |  3.35
+Other   |            | 0.125      |            |       | 18.20
+
+Nlocal:             25 ave          57 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:           5.25 ave          13 max           0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:          38.75 ave          96 max           0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 155
+Ave neighs/atom = 1.55
+Neighbor list builds = 183
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/gransurf/log.1Jul24.tribox.gran.global.stl.g++.1

@@ -0,0 +1,480 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global surf.tribox.stl hooke                 4000.0 NULL 100.0 NULL 0.5 1
+Reading STL object STL version of surf.tribox from text file surf.tribox.stl
+#fix             20 all surface/global surf.tribox.stl hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 1 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 yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.5878 | 0.5878 | 0.5878 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       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   0.82347039     0.82347039     0.41172861     0.0029850802 
+       500          30   0.76963938     0.76963938     0.38709352     0.0042867255 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          64   0.51325196     0.51325196     0.26472957     0.0045780407 
+       700          64   0.57133229     0.57133229     0.29476966     0.0046847812 
+       800          64   0.630634       0.630634       0.32751956     0.0050038133 
+       900          64   0.54233611     0.54233611     0.28819808     0.0052880896 
+      1000          64   0.48543152     0.48543152     0.26491902     0.0064773948 
+      1100          64   0.47303609     0.47303609     0.2578388      0.0057125611 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          99   0.40053109     0.40053109     0.2195167      0.0081778049 
+      1300          99   0.42696772     0.42696772     0.23049402     0.006385146  
+      1400          99   0.37139574     0.37139574     0.20331799     0.0074485307 
+      1500          99   0.33478846     0.33478846     0.18670496     0.0061673941 
+      1600          99   0.29982872     0.29982872     0.16693769     0.0051747985 
+      1700         100   0.2069625      0.2069625      0.12302495     0.005783623  
+      1800         100   0.12902068     0.12902068     0.08608601     0.0019792233 
+      1900         100   0.080857094    0.080857094    0.059672509    0.0022973108 
+      2000         100   0.064403955    0.064403955    0.046429731    0.0011922926 
+      2100         100   0.056475498    0.056475498    0.038678923    0.00085304992
+      2200         100   0.050018256    0.050018256    0.034384821    0.0032112539 
+      2300         100   0.021868304    0.021868304    0.017658151    0.0011526373 
+      2400         100   0.022189236    0.022189236    0.016714436    0.00056488482
+      2500         100   0.012569738    0.012569738    0.010200523    0.00061305414
+      2600         100   0.010861951    0.010861951    0.0086986505   0.00028075976
+      2700         100   0.0092647871   0.0092647871   0.0071124847   0.00043064637
+      2800         100   0.0078527688   0.0078527688   0.0059155703   0.00016902461
+      2900         100   0.0048376734   0.0048376734   0.0039864566   9.6898167e-05
+      3000         100   0.004997394    0.004997394    0.0038195379   0.00012912771
+      3100         100   0.0025381263   0.0025381263   0.0022290621   9.3139494e-05
+      3200         100   0.0023614621   0.0023614621   0.0020627353   0.00043394794
+      3300         100   0.0018926758   0.0018926758   0.0016726508   9.015816e-05 
+      3400         100   0.0016956727   0.0016956727   0.0015060379   9.8437955e-05
+      3500         100   0.0020822011   0.0020822011   0.0016148425   6.8104893e-05
+      3600         100   0.0010660921   0.0010660921   0.0010106443  -4.0921854e-05
+      3700         100   0.00093117128  0.00093117128  0.00086120243  3.9299397e-05
+      3800         100   0.00083426775  0.00083426775  0.00075721786  3.2376e-05   
+      3900         100   0.00076790351  0.00076790351  0.00070733354  3.2793518e-05
+      4000         100   0.0006859536   0.0006859536   0.00062258677  3.0547763e-05
+      4100         100   0.00050291116  0.00050291116  0.00047200581  0.00015040263
+      4200         100   0.00038735513  0.00038735513  0.0003849192   0.00017016843
+      4300         100   0.00031672623  0.00031672623  0.00032789248  7.1880229e-05
+      4400         100   0.00027595545  0.00027595545  0.00029274116  3.120052e-05 
+      4500         100   0.00027092394  0.00027092394  0.00028257706  4.1409733e-05
+      4600         100   0.00026641048  0.00026641048  0.00027631265  3.2258687e-05
+      4700         100   0.0002550395   0.0002550395   0.00026456068  4.4752996e-05
+      4800         100   0.00023866037  0.00023866037  0.00025120225  3.3651155e-05
+      4900         100   0.00019734428  0.00019734428  0.0002099377   2.7700004e-05
+      5000         100   0.00019733184  0.00019733184  0.00020831062  2.6903281e-05
+Loop time of 0.386048 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5595156.861 tau/day, 12951.752 timesteps/s, 1.295 Matom-step/s
+90.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0037007  | 0.0037007  | 0.0037007  |   0.0 |  0.96
+Neigh   | 0.0054702  | 0.0054702  | 0.0054702  |   0.0 |  1.42
+Comm    | 0.0003645  | 0.0003645  | 0.0003645  |   0.0 |  0.09
+Output  | 0.32257    | 0.32257    | 0.32257    |   0.0 | 83.56
+Modify  | 0.052819   | 0.052819   | 0.052819   |   0.0 | 13.68
+Other   |            | 0.001123   |            |       |  0.29
+
+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:            160 ave         160 max         160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 160
+Ave neighs/atom = 1.6
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00019733184  0.00019733184  0.00020831062  2.6930089e-05
+      5100         100   0.14755911     0.14755911     0.085321575    0.0037275005 
+      5200         100   0.17345004     0.17345004     0.10013131     0.0029005613 
+      5300         100   0.17839393     0.17839393     0.09955336     0.0024744353 
+      5400         100   0.18892743     0.18892743     0.10178919     0.0032939874 
+      5500         100   0.19613791     0.19613791     0.10380256     0.0027253339 
+      5600         100   0.19978293     0.19978293     0.10442183     0.0031193701 
+      5700         100   0.21239814     0.21239814     0.10965684     0.0027404998 
+      5800         100   0.22432265     0.22432265     0.11476437     0.0031430877 
+      5900         100   0.22942225     0.22942225     0.11733388     0.00357628   
+      6000         100   0.24043354     0.24043354     0.12272731     0.003255827  
+      6100         100   0.25159401     0.25159401     0.1279307      0.0040378705 
+      6200         100   0.25902708     0.25902708     0.13158752     0.0036512959 
+      6300         100   0.2659723      0.2659723      0.13535001     0.0037298324 
+      6400         100   0.27607055     0.27607055     0.14001655     0.0043863861 
+      6500         100   0.28259585     0.28259585     0.14337861     0.004432214  
+      6600         100   0.29041535     0.29041535     0.14658628     0.0041374757 
+      6700         100   0.29338383     0.29338383     0.14816762     0.0043726723 
+      6800         100   0.29363497     0.29363497     0.14803605     0.0048496941 
+      6900         100   0.29819446     0.29819446     0.14992058     0.0048661826 
+      7000         100   0.30253288     0.30253288     0.15178707     0.0047893404 
+      7100         100   0.30364521     0.30364521     0.15238027     0.0053735204 
+      7200         100   0.30571022     0.30571022     0.15341639     0.0050547621 
+      7300         100   0.30762729     0.30762729     0.15433251     0.0048579985 
+      7400         100   0.30739457     0.30739457     0.15429161     0.0052840169 
+      7500         100   0.3095106      0.3095106      0.15546551     0.0047742904 
+      7600         100   0.30994994     0.30994994     0.15560402     0.0055289317 
+      7700         100   0.3102136      0.3102136      0.1555494      0.0053911148 
+      7800         100   0.31109652     0.31109652     0.15598755     0.0050957646 
+      7900         100   0.31190144     0.31190144     0.15640137     0.0050144069 
+      8000         100   0.3124433      0.3124433      0.15676067     0.0049291948 
+      8100         100   0.31255831     0.31255831     0.15682783     0.0053772662 
+      8200         100   0.31276764     0.31276764     0.15700445     0.0051137616 
+      8300         100   0.31476621     0.31476621     0.15777763     0.0050115786 
+      8400         100   0.31520108     0.31520108     0.1579466      0.0052663181 
+      8500         100   0.31519638     0.31519638     0.15797839     0.0054592691 
+      8600         100   0.31650736     0.31650736     0.15853548     0.006061159  
+      8700         100   0.31783185     0.31783185     0.15910269     0.0055642729 
+      8800         100   0.31962922     0.31962922     0.15981552     0.0051073677 
+      8900         100   0.32028059     0.32028059     0.16016593     0.0051129724 
+      9000         100   0.32067355     0.32067355     0.16033852     0.005334504  
+      9100         100   0.32073134     0.32073134     0.16036476     0.0052193698 
+      9200         100   0.32149618     0.32149618     0.16073834     0.0051959338 
+      9300         100   0.32200413     0.32200413     0.16101431     0.0053371119 
+      9400         100   0.32243427     0.32243427     0.16127313     0.0051442587 
+      9500         100   0.32287887     0.32287887     0.16159452     0.0051133998 
+      9600         100   0.32358279     0.32358279     0.16193072     0.0051698096 
+      9700         100   0.32486591     0.32486591     0.16249108     0.0052421695 
+      9800         100   0.32481094     0.32481094     0.16244971     0.0052881334 
+      9900         100   0.32619742     0.32619742     0.16300857     0.0056091381 
+     10000         100   0.32685101     0.32685101     0.16333907     0.0052565109 
+Loop time of 0.400348 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5395307.917 tau/day, 12489.139 timesteps/s, 1.249 Matom-step/s
+96.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.011048   | 0.011048   | 0.011048   |   0.0 |  2.76
+Neigh   | 0.0070234  | 0.0070234  | 0.0070234  |   0.0 |  1.75
+Comm    | 0.00040106 | 0.00040106 | 0.00040106 |   0.0 |  0.10
+Output  | 0.3144     | 0.3144     | 0.3144     |   0.0 | 78.53
+Modify  | 0.066249   | 0.066249   | 0.066249   |   0.0 | 16.55
+Other   |            | 0.001222   |            |       |  0.31
+
+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:            190 ave         190 max         190 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 190
+Ave neighs/atom = 1.9
+Neighbor list builds = 334
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   0.32685101     0.32685101     0.16333907     0.0052114688 
+     10100         100   0.082150677    0.082150677    0.051495507    0.0065164512 
+     10200         100   0.044140364    0.044140364    0.034724328    0.0010465239 
+     10300         100   0.033122648    0.033122648    0.026625827    0.0022974917 
+     10400         100   0.026649705    0.026649705    0.021846707    0.00035032509
+     10500         100   0.022611369    0.022611369    0.018405546    0.0004069116 
+     10600         100   0.018296124    0.018296124    0.014829351    0.00026270833
+     10700         100   0.015248747    0.015248747    0.012084705    0.00023227455
+     10800         100   0.014989372    0.014989372    0.011849067    0.00054473331
+     10900         100   0.011865503    0.011865503    0.0094526639   0.00028431427
+     11000         100   0.0096206477   0.0096206477   0.0077795159   0.00012996686
+     11100         100   0.0085270379   0.0085270379   0.0069458369   0.00021692214
+     11200         100   0.00760939     0.00760939     0.0062336019   0.00015816658
+     11300         100   0.0070094711   0.0070094711   0.0056987409   9.7160075e-05
+     11400         100   0.0064681327   0.0064681327   0.0053334513   0.0001693687 
+     11500         100   0.0054400476   0.0054400476   0.0044705267   8.1382559e-05
+     11600         100   0.005206949    0.005206949    0.0042892806   7.0309283e-05
+     11700         100   0.0044637648   0.0044637648   0.0037251717   5.4172517e-05
+     11800         100   0.0039969168   0.0039969168   0.003362444    2.0226315e-05
+     11900         100   0.0033117132   0.0033117132   0.0027762101   5.2311253e-05
+     12000         100   0.0031073405   0.0031073405   0.0025984799   3.9890528e-05
+     12100         100   0.0029847617   0.0029847617   0.0025070771  -5.7259344e-06
+     12200         100   0.0028458878   0.0028458878   0.0024108535   3.5217862e-05
+     12300         100   0.0026501923   0.0026501923   0.0022711794   0.00012033569
+     12400         100   0.0025425504   0.0025425504   0.0021847643   3.1464061e-05
+     12500         100   0.0024161319   0.0024161319   0.0020843813   0.00014941327
+     12600         100   0.002341327    0.002341327    0.0020232445   2.8973921e-05
+     12700         100   0.0022334192   0.0022334192   0.0019425572   3.0790164e-05
+     12800         100   0.0021889403   0.0021889403   0.0019088353   2.9638662e-05
+     12900         100   0.0020442842   0.0020442842   0.0018049012   2.5298016e-05
+     13000         100   0.001803154    0.001803154    0.0016328702   2.2314031e-05
+     13100         100   0.0016791405   0.0016791405   0.0015327583   2.2967562e-05
+     13200         100   0.001622137    0.001622137    0.0014810169   4.0326561e-05
+     13300         100   0.001601531    0.001601531    0.0014650816   1.9818946e-05
+     13400         100   0.0015591399   0.0015591399   0.0014123726   2.119773e-05 
+     13500         100   0.0014546357   0.0014546357   0.0013328423   1.8001117e-05
+     13600         100   0.0013998773   0.0013998773   0.0012913696   2.6202181e-05
+     13700         100   0.001367574    0.001367574    0.0012631494   1.6923729e-05
+     13800         100   0.001225732    0.001225732    0.0011125165   1.4445147e-05
+     13900         100   0.0012086291   0.0012086291   0.0010972374   2.8597468e-05
+     14000         100   0.0011916306   0.0011916306   0.0010833978   7.2381933e-05
+     14100         100   0.0011461149   0.0011461149   0.0010110271   1.4183172e-05
+     14200         100   0.0011209785   0.0011209785   0.00099190436  1.1546608e-05
+     14300         100   0.0011050802   0.0011050802   0.00098070422  1.3675367e-05
+     14400         100   0.0010910417   0.0010910417   0.00097025303  1.3501641e-05
+     14500         100   0.0010645152   0.0010645152   0.00093785696  1.3173375e-05
+     14600         100   0.0010479185   0.0010479185   0.00092353031  2.5164629e-05
+     14700         100   0.00099034477  0.00099034477  0.0008638973   1.2874356e-05
+     14800         100   0.00099115544  0.00099115544  0.00086195396  1.2265549e-05
+     14900         100   0.00097510619  0.00097510619  0.00083043649  6.0289327e-05
+     15000         100   0.00095883902  0.00095883902  0.00080522184  1.1865633e-05
+Loop time of 0.392742 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5499795.998 tau/day, 12731.009 timesteps/s, 1.273 Matom-step/s
+95.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0032195  | 0.0032195  | 0.0032195  |   0.0 |  0.82
+Neigh   | 0.0014096  | 0.0014096  | 0.0014096  |   0.0 |  0.36
+Comm    | 0.00031448 | 0.00031448 | 0.00031448 |   0.0 |  0.08
+Output  | 0.32823    | 0.32823    | 0.32823    |   0.0 | 83.57
+Modify  | 0.058394   | 0.058394   | 0.058394   |   0.0 | 14.87
+Other   |            | 0.001171   |            |       |  0.30
+
+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:            165 ave         165 max         165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 165
+Ave neighs/atom = 1.65
+Neighbor list builds = 69
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00095883902  0.00095883902  0.00080522184  1.1865633e-05
+     15100         100   0.16225441     0.16225441     0.098498099    0.0064159333 
+     15200         100   0.22482098     0.22482098     0.12948232     0.003576331  
+     15300         100   0.2458026      0.2458026      0.1393646      0.006749306  
+     15400         100   0.26239222     0.26239222     0.1469859      0.0089800228 
+     15500         100   0.28687382     0.28687382     0.15847135     0.0079704333 
+     15600         100   0.28622953     0.28622953     0.15902139     0.0082281462 
+     15700         100   0.30668089     0.30668089     0.16265483     0.014688893  
+     15800         100   0.33007713     0.33007713     0.17247344     0.0099574571 
+     15900         100   0.35773029     0.35773029     0.18298391     0.01415523   
+     16000         100   0.36309971     0.36309971     0.18514042     0.010763173  
+     16100         100   0.36974105     0.36974105     0.18746237     0.010738235  
+     16200         100   0.36988383     0.36988383     0.18775314     0.014768427  
+     16300         100   0.37560588     0.37560588     0.19010652     0.014297415  
+     16400         100   0.37747146     0.37747146     0.19143031     0.014086853  
+     16500         100   0.38053331     0.38053331     0.19248441     0.01837541   
+     16600         100   0.37315821     0.37315821     0.1881627      0.0098076132 
+     16700         100   0.38286964     0.38286964     0.19289589     0.011785316  
+     16800         100   0.38013501     0.38013501     0.19200912     0.0138546    
+     16900         100   0.37496008     0.37496008     0.19035729     0.010235176  
+     17000         100   0.365244       0.365244       0.18508129     0.011814705  
+     17100         100   0.36324363     0.36324363     0.18539176     0.0077602876 
+     17200         100   0.36563128     0.36563128     0.18828717     0.009760622  
+     17300         100   0.41040797     0.41040797     0.21297576     0.0060030421 
+     17400         100   0.42784496     0.42784496     0.22357917     0.0072328321 
+     17500         100   0.44480315     0.44480315     0.23296103     0.0081208771 
+     17600         100   0.49540498     0.49540498     0.26207461     0.0094193362 
+     17700         100   0.53563972     0.53563972     0.28429788     0.0096153439 
+     17800         100   0.59909402     0.59909402     0.31832665     0.0086897236 
+     17900         100   0.65975736     0.65975736     0.35361646     0.010946403  
+     18000         100   0.67883738     0.67883738     0.36868438     0.010453697  
+     18100         100   0.67229859     0.67229859     0.37009573     0.011447688  
+     18200         100   0.58740281     0.58740281     0.32918911     0.012430038  
+     18300         100   0.51321184     0.51321184     0.29212329     0.014782894  
+     18400         100   0.46432678     0.46432678     0.26861208     0.0074401518 
+     18500         100   0.46083979     0.46083979     0.26638884     0.0090587319 
+     18600         100   0.41968764     0.41968764     0.24616432     0.0091476182 
+     18700         100   0.40749768     0.40749768     0.24073731     0.0073954099 
+     18800         100   0.38490007     0.38490007     0.23057035     0.0056617504 
+     18900         100   0.36115679     0.36115679     0.21996888     0.0069095868 
+     19000         100   0.31118149     0.31118149     0.19549915     0.0066423887 
+     19100         100   0.34419249     0.34419249     0.20736311     0.012418102  
+     19200         100   0.33174248     0.33174248     0.19629654     0.0074405926 
+     19300         100   0.33028394     0.33028394     0.19472996     0.0077286569 
+     19400         100   0.33612501     0.33612501     0.19522775     0.0083424841 
+     19500         100   0.32216161     0.32216161     0.18401278     0.0088692814 
+     19600         100   0.33681829     0.33681829     0.18758804     0.0097379383 
+     19700         100   0.33730835     0.33730835     0.18474995     0.009296681  
+     19800         100   0.3351213      0.3351213      0.18164387     0.0061672199 
+     19900         100   0.32674396     0.32674396     0.17780137     0.0062277401 
+     20000         100   0.31549601     0.31549601     0.17276762     0.011954545  
+Loop time of 0.420421 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5137707.802 tau/day, 11892.842 timesteps/s, 1.189 Matom-step/s
+97.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.010253   | 0.010253   | 0.010253   |   0.0 |  2.44
+Neigh   | 0.010525   | 0.010525   | 0.010525   |   0.0 |  2.50
+Comm    | 0.00042181 | 0.00042181 | 0.00042181 |   0.0 |  0.10
+Output  | 0.33826    | 0.33826    | 0.33826    |   0.0 | 80.46
+Modify  | 0.059694   | 0.059694   | 0.059694   |   0.0 | 14.20
+Other   |            | 0.001267   |            |       |  0.30
+
+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:            242 ave         242 max         242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 242
+Ave neighs/atom = 2.42
+Neighbor list builds = 435
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.714 | 4.714 | 4.714 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   0.31549601     0.31549601     0.17276762     0.011924862  
+     20100         100   0.067243668    0.067243668    0.051058315    0.0026847669 
+     20200         100   0.064954648    0.064954648    0.04577406     0.0031985925 
+     20300         100   0.081722159    0.081722159    0.052328099    0.003382093  
+     20400         100   0.052538018    0.052538018    0.038041695    0.0080953559 
+     20500         100   0.045138106    0.045138106    0.032227169    0.0035839274 
+     20600         100   0.044187088    0.044187088    0.031849801    0.0032417719 
+     20700         100   0.048791318    0.048791318    0.033838035    0.0030783015 
+     20800         100   0.042228029    0.042228029    0.029496426    0.0026771471 
+     20900         100   0.037884649    0.037884649    0.026659395    0.0016131444 
+     21000         100   0.036121934    0.036121934    0.025961479    0.0033546991 
+     21100         100   0.041151215    0.041151215    0.028554924    0.0014986709 
+     21200         100   0.032352882    0.032352882    0.024166876    0.0018674452 
+     21300         100   0.033808076    0.033808076    0.02501534     0.0014150028 
+     21400         100   0.033233201    0.033233201    0.024762604    0.0015124318 
+     21500         100   0.023344798    0.023344798    0.017595957    0.0020406313 
+     21600         100   0.024137168    0.024137168    0.017835056    0.001648494  
+     21700         100   0.020201901    0.020201901    0.015367789    0.0014089977 
+     21800         100   0.019279358    0.019279358    0.014625498    0.0012643094 
+     21900         100   0.01893081     0.01893081     0.014292746    0.0015049479 
+     22000         100   0.017257227    0.017257227    0.01315079     0.0011652685 
+     22100         100   0.015479952    0.015479952    0.011715026    0.0014536538 
+     22200         100   0.016610168    0.016610168    0.012253776    0.00089466949
+     22300         100   0.014924039    0.014924039    0.011273468    0.0010494839 
+     22400         100   0.015991668    0.015991668    0.011902404    0.00082344174
+     22500         100   0.011574074    0.011574074    0.0087681303   0.00081009385
+     22600         100   0.012494171    0.012494171    0.0092328529   0.0005622816 
+     22700         100   0.011070984    0.011070984    0.0083661745   0.00080065357
+     22800         100   0.01131513     0.01131513     0.0084259241   0.00073680805
+     22900         100   0.010217077    0.010217077    0.0077647566   0.00053727888
+     23000         100   0.0099409381   0.0099409381   0.0074288509   0.00058448502
+     23100         100   0.0091176585   0.0091176585   0.0069209665   0.00063336231
+     23200         100   0.0083540727   0.0083540727   0.0063805491   0.0005281495 
+     23300         100   0.008619666    0.008619666    0.0065404908   0.0005398125 
+     23400         100   0.0088762213   0.0088762213   0.0065206851   0.00046304022
+     23500         100   0.007364061    0.007364061    0.0055771232   0.00046541178
+     23600         100   0.0074046272   0.0074046272   0.0055598275   0.00036522805
+     23700         100   0.0073881556   0.0073881556   0.0055580858   0.0005353812 
+     23800         100   0.0072954594   0.0072954594   0.0053965497   0.00041955961
+     23900         100   0.006566226    0.006566226    0.0047704154   0.00037213632
+     24000         100   0.0052279617   0.0052279617   0.0039151171   0.00039220479
+     24100         100   0.004661037    0.004661037    0.0035353607   0.00036592087
+     24200         100   0.0046822639   0.0046822639   0.0035561511   0.00036233017
+     24300         100   0.0047878887   0.0047878887   0.0036222045   0.0003906286 
+     24400         100   0.005705559    0.005705559    0.0041298188   0.00039793154
+     24500         100   0.0038440196   0.0038440196   0.0030815263   0.00050064408
+     24600         100   0.0035754817   0.0035754817   0.0030293001   0.00032292161
+     24700         100   0.003446554    0.003446554    0.0027976688   0.00029115924
+     24800         100   0.0028987207   0.0028987207   0.0023988341   0.00018959598
+     24900         100   0.0027083267   0.0027083267   0.0021669208   0.0001799362 
+     25000         100   0.0026561456   0.0026561456   0.0020638865   0.00014386648
+Loop time of 0.399883 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 5401574.775 tau/day, 12503.645 timesteps/s, 1.250 Matom-step/s
+94.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0082229  | 0.0082229  | 0.0082229  |   0.0 |  2.06
+Neigh   | 0.004223   | 0.004223   | 0.004223   |   0.0 |  1.06
+Comm    | 0.0003435  | 0.0003435  | 0.0003435  |   0.0 |  0.09
+Output  | 0.32748    | 0.32748    | 0.32748    |   0.0 | 81.89
+Modify  | 0.058357   | 0.058357   | 0.058357   |   0.0 | 14.59
+Other   |            | 0.001255   |            |       |  0.31
+
+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:            147 ave         147 max         147 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 147
+Ave neighs/atom = 1.47
+Neighbor list builds = 173
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/gransurf/log.1Jul24.tribox.gran.global.stl.g++.4

@@ -0,0 +1,481 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	sphere
+#atom_modify     map array
+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   # simply for dump_modify to color lines = green
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff      * *
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             20 all surface/global surf.tribox.stl hooke                 4000.0 NULL 100.0 NULL 0.5 1
+Reading STL object STL version of surf.tribox from text file surf.tribox.stl
+#fix             20 all surface/global surf.tribox.stl hooke/history #                4000.0 NULL 100.0 NULL 0.5 1
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+#fix             4 all viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 1 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 yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 fix 20 type 2 0.5
+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/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.486 | 0.486 | 0.486 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       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   0.82347039     0.82347039     0.41172861     0.0029850802 
+       500          30   0.76963938     0.76963938     0.38709352     0.0042867255 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          64   0.51325196     0.51325196     0.26472957     0.0045780407 
+       700          64   0.57133229     0.57133229     0.29476966     0.0046847812 
+       800          64   0.630634       0.630634       0.32751956     0.0050038133 
+       900          64   0.54233611     0.54233611     0.28819808     0.0052880896 
+      1000          64   0.48543152     0.48543152     0.26491902     0.0064773948 
+      1100          64   0.47303609     0.47303609     0.2578388      0.0057125611 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200          99   0.40053109     0.40053109     0.2195167      0.0081778049 
+      1300          99   0.42696772     0.42696772     0.23049402     0.006385146  
+      1400          99   0.37139574     0.37139574     0.20331799     0.0074485306 
+      1500          99   0.33478846     0.33478846     0.18670496     0.0061673941 
+      1600          99   0.29982872     0.29982872     0.16693769     0.0051747984 
+      1700         100   0.2069625      0.2069625      0.12302495     0.005783624  
+      1800         100   0.12902068     0.12902068     0.08608601     0.0019792234 
+      1900         100   0.080857095    0.080857095    0.05967251     0.0022973101 
+      2000         100   0.064403959    0.064403959    0.046429734    0.0011922946 
+      2100         100   0.056475466    0.056475466    0.038678907    0.00085302928
+      2200         100   0.050018273    0.050018273    0.03438483     0.0032112547 
+      2300         100   0.02186833     0.02186833     0.01765815     0.001152603  
+      2400         100   0.02218925     0.02218925     0.016714386    0.00056474678
+      2500         100   0.012569988    0.012569988    0.010200648    0.0006133907 
+      2600         100   0.010862479    0.010862479    0.0086989172   0.00028072722
+      2700         100   0.0092737903   0.0092737903   0.0071165383   0.00041430278
+      2800         100   0.0078587709   0.0078587709   0.00592121     0.00017374958
+      2900         100   0.0048613617   0.0048613617   0.004000904    0.00021321956
+      3000         100   0.0050147313   0.0050147313   0.0038322501   0.00017831675
+      3100         100   0.0025550411   0.0025550411   0.0022405824   6.8592843e-05
+      3200         100   0.0023577912   0.0023577912   0.0020418633   0.0003584618 
+      3300         100   0.0018996206   0.0018996206   0.0016777567   7.5165222e-05
+      3400         100   0.001694751    0.001694751    0.0015042348   0.00014566717
+      3500         100   0.0020882068   0.0020882068   0.0016170458   8.7027542e-05
+      3600         100   0.0010813667   0.0010813667   0.0010137349   8.5126382e-05
+      3700         100   0.00094548982  0.00094548982  0.00086966169  4.2409893e-05
+      3800         100   0.00084816181  0.00084816181  0.00077098131  3.011429e-05 
+      3900         100   0.00078382097  0.00078382097  0.00071960486  5.939333e-05 
+      4000         100   0.00075302926  0.00075302926  0.00067851822  3.2758594e-05
+      4100         100   0.00051405526  0.00051405526  0.00048629367  0.00013859285
+      4200         100   0.00038825626  0.00038825626  0.00038868575  0.00020599691
+      4300         100   0.00031919597  0.00031919597  0.00033058576  0.00010854923
+      4400         100   0.00029919941  0.00029919941  0.00031222783  7.2391663e-05
+      4500         100   0.0002903216   0.0002903216   0.00029974662  5.5125563e-05
+      4600         100   0.0002753977   0.0002753977   0.00028258456  9.6552286e-05
+      4700         100   0.00027064725  0.00027064725  0.0002776974   4.0309048e-05
+      4800         100   0.00024203571  0.00024203571  0.00025112727  3.3700422e-05
+      4900         100   0.00020539914  0.00020539914  0.00021705763  2.7873051e-05
+      5000         100   0.00018816565  0.00018816565  0.00020135634  4.7752851e-05
+Loop time of 0.542754 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3979701.998 tau/day, 9212.273 timesteps/s, 921.227 katom-step/s
+97.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00023334 | 0.0013294  | 0.0024933  |   3.0 |  0.24
+Neigh   | 0.0014051  | 0.0023307  | 0.0035103  |   1.7 |  0.43
+Comm    | 0.0076195  | 0.011811   | 0.015893   |   3.6 |  2.18
+Output  | 0.36521    | 0.41573    | 0.48288    |   7.3 | 76.60
+Modify  | 0.0021283  | 0.017049   | 0.034423   |  11.4 |  3.14
+Other   |            | 0.09451    |            |       | 17.41
+
+Nlocal:             25 ave          50 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            4.5 ave           9 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           40.5 ave          82 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 162
+Ave neighs/atom = 1.62
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.549 | 4.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00018816565  0.00018816565  0.00020135634  4.4246792e-05
+      5100         100   0.14937779     0.14937779     0.086114773    0.0025984359 
+      5200         100   0.17697193     0.17697193     0.1019691      0.0026173891 
+      5300         100   0.18255024     0.18255024     0.10122134     0.0041759269 
+      5400         100   0.19510207     0.19510207     0.1050284      0.0027541295 
+      5500         100   0.1980801      0.1980801      0.10458743     0.0027957101 
+      5600         100   0.20490362     0.20490362     0.10674522     0.002985542  
+      5700         100   0.21087885     0.21087885     0.10861062     0.0030935481 
+      5800         100   0.22309411     0.22309411     0.11419601     0.0029760547 
+      5900         100   0.22880189     0.22880189     0.1171042      0.0029681474 
+      6000         100   0.2363739      0.2363739      0.12083453     0.0032437464 
+      6100         100   0.24581768     0.24581768     0.12531649     0.0032571271 
+      6200         100   0.25161424     0.25161424     0.12838601     0.0034995369 
+      6300         100   0.25972194     0.25972194     0.13241738     0.0035882457 
+      6400         100   0.2678312      0.2678312      0.13632033     0.0036612131 
+      6500         100   0.27990358     0.27990358     0.14189324     0.0046486676 
+      6600         100   0.2827759      0.2827759      0.14317296     0.0048164853 
+      6700         100   0.2897351      0.2897351      0.14616568     0.0042753049 
+      6800         100   0.29164978     0.29164978     0.14688678     0.0040397004 
+      6900         100   0.29377421     0.29377421     0.14786359     0.0051561937 
+      7000         100   0.29698841     0.29698841     0.14947643     0.0046008044 
+      7100         100   0.3019081      0.3019081      0.15147175     0.0065696769 
+      7200         100   0.30532028     0.30532028     0.1531023      0.0045987829 
+      7300         100   0.30629289     0.30629289     0.15368598     0.0048558556 
+      7400         100   0.30534641     0.30534641     0.15316839     0.0057637671 
+      7500         100   0.30786877     0.30786877     0.15429461     0.004843753  
+      7600         100   0.30862009     0.30862009     0.15464621     0.0052118056 
+      7700         100   0.30900657     0.30900657     0.15478242     0.0048879932 
+      7800         100   0.31054034     0.31054034     0.1554636      0.0052082034 
+      7900         100   0.31174887     0.31174887     0.15610325     0.0049178073 
+      8000         100   0.31247071     0.31247071     0.15647921     0.0052603626 
+      8100         100   0.31273024     0.31273024     0.15659099     0.0056001647 
+      8200         100   0.3140235      0.3140235      0.15727592     0.004977821  
+      8300         100   0.31383701     0.31383701     0.15715969     0.0052231004 
+      8400         100   0.31509644     0.31509644     0.15775385     0.0050051889 
+      8500         100   0.31498521     0.31498521     0.15762151     0.0052864908 
+      8600         100   0.31575201     0.31575201     0.15792624     0.0050759547 
+      8700         100   0.31620758     0.31620758     0.15818292     0.0050530619 
+      8800         100   0.31691036     0.31691036     0.15860213     0.005004857  
+      8900         100   0.31659627     0.31659627     0.15846212     0.0050695163 
+      9000         100   0.31769151     0.31769151     0.15903638     0.0050507355 
+      9100         100   0.31716143     0.31716143     0.15881355     0.005017094  
+      9200         100   0.31633956     0.31633956     0.1585031      0.0053446628 
+      9300         100   0.31655443     0.31655443     0.15863537     0.0049328007 
+      9400         100   0.31599503     0.31599503     0.15822485     0.0049933297 
+      9500         100   0.31660281     0.31660281     0.15853731     0.0049387958 
+      9600         100   0.31664518     0.31664518     0.15861539     0.0049222414 
+      9700         100   0.31824803     0.31824803     0.15934333     0.0052873464 
+      9800         100   0.31820192     0.31820192     0.15932994     0.0049687062 
+      9900         100   0.31846082     0.31846082     0.15943054     0.0053817995 
+     10000         100   0.31969811     0.31969811     0.15997735     0.005012462  
+Loop time of 0.522575 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 4133381.630 tau/day, 9568.013 timesteps/s, 956.801 katom-step/s
+96.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00017938 | 0.0034898  | 0.0074454  |   5.6 |  0.67
+Neigh   | 0.0013735  | 0.0028718  | 0.0047582  |   2.8 |  0.55
+Comm    | 0.0060132  | 0.009996   | 0.014865   |   3.9 |  1.91
+Output  | 0.34648    | 0.38923    | 0.45057    |   6.7 | 74.48
+Modify  | 0.0022557  | 0.02188    | 0.043145   |  13.2 |  4.19
+Other   |            | 0.09511    |            |       | 18.20
+
+Nlocal:             25 ave          52 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4.25 ave           9 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:           47.5 ave         111 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 190
+Ave neighs/atom = 1.9
+Neighbor list builds = 334
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.549 | 4.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   0.31969811     0.31969811     0.15997735     0.005039886  
+     10100         100   0.096856693    0.096856693    0.061256799    0.0017653508 
+     10200         100   0.06374563     0.06374563     0.049164989    0.00074375479
+     10300         100   0.053346958    0.053346958    0.041648676    0.00088021828
+     10400         100   0.04530167     0.04530167     0.035468031    0.0006357307 
+     10500         100   0.036511473    0.036511473    0.02864095     0.00046569718
+     10600         100   0.031850796    0.031850796    0.024752197    0.001484525  
+     10700         100   0.027853481    0.027853481    0.021856016    0.00083233598
+     10800         100   0.023988298    0.023988298    0.018551491    0.00025321878
+     10900         100   0.022362927    0.022362927    0.01775739     0.00027674123
+     11000         100   0.019598739    0.019598739    0.01566657     0.00029114873
+     11100         100   0.016949467    0.016949467    0.013323455    0.00054759179
+     11200         100   0.013201141    0.013201141    0.010205793    0.00046859829
+     11300         100   0.010724903    0.010724903    0.0083548813   0.00016110668
+     11400         100   0.0094528501   0.0094528501   0.0074254702   0.00012282294
+     11500         100   0.0081681904   0.0081681904   0.0064435379   0.00018389596
+     11600         100   0.0080112061   0.0080112061   0.006319339    9.9138675e-05
+     11700         100   0.0072316886   0.0072316886   0.0056968863   8.9492146e-05
+     11800         100   0.0066741475   0.0066741475   0.0052653282   9.1792343e-05
+     11900         100   0.0060596979   0.0060596979   0.0048019244   0.00059435717
+     12000         100   0.0058193298   0.0058193298   0.0046098949   7.2231759e-05
+     12100         100   0.0053847114   0.0053847114   0.0042545862   9.3394135e-05
+     12200         100   0.0049412476   0.0049412476   0.0039106158   0.00010078502
+     12300         100   0.004572105    0.004572105    0.0036504695   5.5867397e-05
+     12400         100   0.0042412045   0.0042412045   0.0034175496   0.00036582163
+     12500         100   0.0035923846   0.0035923846   0.0029316243   6.9114212e-05
+     12600         100   0.0032446947   0.0032446947   0.0026668677   4.1659699e-05
+     12700         100   0.003132735    0.003132735    0.0025875973   5.6802791e-05
+     12800         100   0.0030486242   0.0030486242   0.0025160882   0.00024777199
+     12900         100   0.0029017497   0.0029017497   0.0024179283   6.7491687e-05
+     13000         100   0.0027960043   0.0027960043   0.0023415783   3.4600553e-05
+     13100         100   0.0024698607   0.0024698607   0.0020868913   0.00015330841
+     13200         100   0.0023835355   0.0023835355   0.0020283653   2.9496252e-05
+     13300         100   0.0021088439   0.0021088439   0.0018016867   5.3026287e-05
+     13400         100   0.0018955838   0.0018955838   0.0016251265   5.6464898e-05
+     13500         100   0.0017787595   0.0017787595   0.0015273835   0.00010533321
+     13600         100   0.0017398053   0.0017398053   0.0015003761   2.153009e-05 
+     13700         100   0.0017070216   0.0017070216   0.0014780376   2.2369503e-05
+     13800         100   0.0016227474   0.0016227474   0.0014210693   6.9106097e-05
+     13900         100   0.0016020414   0.0016020414   0.0013971016   1.9825262e-05
+     14000         100   0.0015849364   0.0015849364   0.0013841731   1.9613588e-05
+     14100         100   0.0014802906   0.0014802906   0.001301188    2.3602632e-05
+     14200         100   0.0014452784   0.0014452784   0.0012723611   5.4930779e-05
+     14300         100   0.0013373933   0.0013373933   0.0011970238   7.7331197e-05
+     14400         100   0.0012644873   0.0012644873   0.0011371743   3.3804604e-05
+     14500         100   0.0012269172   0.0012269172   0.0011090464   0.00019066733
+     14600         100   0.0011790378   0.0011790378   0.0010710915   2.2152438e-05
+     14700         100   0.001141029    0.001141029    0.0010389261   1.4725855e-05
+     14800         100   0.001136936    0.001136936    0.0010350762   1.833013e-05 
+     14900         100   0.0010587639   0.0010587639   0.00097375352  1.3102203e-05
+     15000         100   0.0010255325   0.0010255325   0.00094590806  1.5126454e-05
+Loop time of 0.518427 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 4166449.618 tau/day, 9644.559 timesteps/s, 964.456 katom-step/s
+96.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00015995 | 0.0012056  | 0.0023882  |   3.0 |  0.23
+Neigh   | 0.00040855 | 0.00070112 | 0.0010401  |   0.0 |  0.14
+Comm    | 0.0011854  | 0.0064387  | 0.011735   |   6.5 |  1.24
+Output  | 0.35648    | 0.4008     | 0.4616     |   6.5 | 77.31
+Modify  | 0.00044023 | 0.018312   | 0.038465   |  13.3 |  3.53
+Other   |            | 0.09097    |            |       | 17.55
+
+Nlocal:             25 ave          50 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4.25 ave          10 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:             37 ave          77 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 148
+Ave neighs/atom = 1.48
+Neighbor list builds = 72
+Dangerous builds = 0
+
+fix_modify      20 move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.549 | 4.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.0010255325   0.0010255325   0.00094590806  1.4814045e-05
+     15100         100   0.16111221     0.16111221     0.097982105    0.0056716878 
+     15200         100   0.21347296     0.21347296     0.12567019     0.0029815056 
+     15300         100   0.24705334     0.24705334     0.13884473     0.0078448562 
+     15400         100   0.27522493     0.27522493     0.15035782     0.0073215473 
+     15500         100   0.30348486     0.30348486     0.16433701     0.0068229641 
+     15600         100   0.31550013     0.31550013     0.16857649     0.0077789307 
+     15700         100   0.32318922     0.32318922     0.1719013      0.012280847  
+     15800         100   0.33908701     0.33908701     0.17750923     0.015821994  
+     15900         100   0.35593866     0.35593866     0.18345193     0.021263374  
+     16000         100   0.36889801     0.36889801     0.1869234      0.011456078  
+     16100         100   0.35809835     0.35809835     0.18158992     0.014811103  
+     16200         100   0.36319635     0.36319635     0.18337159     0.012823323  
+     16300         100   0.35852464     0.35852464     0.18081456     0.01280934   
+     16400         100   0.34902631     0.34902631     0.17663396     0.012992629  
+     16500         100   0.33443513     0.33443513     0.16948607     0.012986886  
+     16600         100   0.3150597      0.3150597      0.16079097     0.010586882  
+     16700         100   0.31338609     0.31338609     0.16045733     0.009805616  
+     16800         100   0.30473867     0.30473867     0.15686705     0.014362545  
+     16900         100   0.31270607     0.31270607     0.16119766     0.0070575979 
+     17000         100   0.2832931      0.2832931      0.14785887     0.0039466166 
+     17100         100   0.28215868     0.28215868     0.14795001     0.0068627045 
+     17200         100   0.29701033     0.29701033     0.16099476     0.0040667324 
+     17300         100   0.3665611      0.3665611      0.19664166     0.0065836505 
+     17400         100   0.43400548     0.43400548     0.23335072     0.0096693511 
+     17500         100   0.5057676      0.5057676      0.2773349      0.0071479313 
+     17600         100   0.52614351     0.52614351     0.29090432     0.0095749902 
+     17700         100   0.52478022     0.52478022     0.29525839     0.010528327  
+     17800         100   0.53046479     0.53046479     0.29862674     0.012410569  
+     17900         100   0.51722354     0.51722354     0.29212965     0.0097423802 
+     18000         100   0.51837131     0.51837131     0.29426864     0.010265508  
+     18100         100   0.46407283     0.46407283     0.26786292     0.015842602  
+     18200         100   0.4281392      0.4281392      0.24883206     0.016085526  
+     18300         100   0.36407304     0.36407304     0.22014997     0.0091448904 
+     18400         100   0.32800292     0.32800292     0.20387181     0.0088602724 
+     18500         100   0.30727965     0.30727965     0.18744751     0.0067928429 
+     18600         100   0.31715182     0.31715182     0.19306784     0.0047252497 
+     18700         100   0.29383189     0.29383189     0.18450238     0.0046337396 
+     18800         100   0.28365185     0.28365185     0.1810902      0.005644391  
+     18900         100   0.30670015     0.30670015     0.19521314     0.0048593554 
+     19000         100   0.31681967     0.31681967     0.201889       0.0059511233 
+     19100         100   0.32218287     0.32218287     0.20009306     0.0093378277 
+     19200         100   0.30255724     0.30255724     0.19160821     0.0087838518 
+     19300         100   0.31907942     0.31907942     0.19849225     0.0093802566 
+     19400         100   0.31650176     0.31650176     0.18834128     0.010429547  
+     19500         100   0.32959296     0.32959296     0.19229144     0.012724502  
+     19600         100   0.33134974     0.33134974     0.18581781     0.016960866  
+     19700         100   0.32878109     0.32878109     0.18215506     0.0096165803 
+     19800         100   0.33724696     0.33724696     0.18335211     0.0060443045 
+     19900         100   0.33179464     0.33179464     0.17822307     0.010776083  
+     20000         100   0.34377432     0.34377432     0.1841787      0.0094534745 
+Loop time of 0.554453 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 3895732.487 tau/day, 9017.899 timesteps/s, 901.790 katom-step/s
+96.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00041707 | 0.0030836  | 0.0058653  |   4.5 |  0.56
+Neigh   | 0.0023165  | 0.0042879  | 0.0074847  |   3.2 |  0.77
+Comm    | 0.020096   | 0.023667   | 0.026287   |   1.5 |  4.27
+Output  | 0.36416    | 0.41297    | 0.47377    |   6.5 | 74.48
+Modify  | 0.0054574  | 0.020137   | 0.037629   |  10.0 |  3.63
+Other   |            | 0.09031    |            |       | 16.29
+
+Nlocal:             25 ave          67 max           0 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:           6.25 ave          13 max           0 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:          54.75 ave         156 max           0 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 219
+Ave neighs/atom = 2.19
+Neighbor list builds = 430
+Dangerous builds = 0
+
+fix_modify      20 move none
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.612 | 4.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   0.34377432     0.34377432     0.1841787      0.0092764528 
+     20100         100   0.097239014    0.097239014    0.068864895    0.0029157234 
+     20200         100   0.090387219    0.090387219    0.063243792    0.0030276724 
+     20300         100   0.10130213     0.10130213     0.065604495    0.0040954401 
+     20400         100   0.073193003    0.073193003    0.049395297    0.011005746  
+     20500         100   0.064987626    0.064987626    0.042476486    0.0035623578 
+     20600         100   0.056092845    0.056092845    0.035733351    0.0046843988 
+     20700         100   0.047975467    0.047975467    0.031279933    0.006027     
+     20800         100   0.042713655    0.042713655    0.028630415    0.0028623851 
+     20900         100   0.027009619    0.027009619    0.019950334    0.0031930947 
+     21000         100   0.030115735    0.030115735    0.021837467    0.0031118498 
+     21100         100   0.030382146    0.030382146    0.02158358     0.0016950638 
+     21200         100   0.028917881    0.028917881    0.020618558    0.0015449848 
+     21300         100   0.02553423     0.02553423     0.018753907    0.0020401097 
+     21400         100   0.024907599    0.024907599    0.018805009    0.0015219354 
+     21500         100   0.028047498    0.028047498    0.020431592    0.0036172877 
+     21600         100   0.023143766    0.023143766    0.017048059    0.001391321  
+     21700         100   0.025832817    0.025832817    0.018907239    0.0014196777 
+     21800         100   0.02294723     0.02294723     0.016986932    0.00099306999
+     21900         100   0.021774769    0.021774769    0.016357385    0.0015445184 
+     22000         100   0.019488798    0.019488798    0.014411675    0.00096975376
+     22100         100   0.017498173    0.017498173    0.013303102    0.0013869769 
+     22200         100   0.017606431    0.017606431    0.013696534    0.0016275912 
+     22300         100   0.01864478     0.01864478     0.014363082    0.00093199338
+     22400         100   0.017184319    0.017184319    0.013013426    0.0007137204 
+     22500         100   0.016970049    0.016970049    0.012735761    0.00094285653
+     22600         100   0.015601151    0.015601151    0.011558366    0.00064664867
+     22700         100   0.01532704     0.01532704     0.011052585    0.0011443538 
+     22800         100   0.013843117    0.013843117    0.010175224    0.00074058068
+     22900         100   0.0142626      0.0142626      0.010517503    0.00062291367
+     23000         100   0.012672457    0.012672457    0.0095213548   0.00048253765
+     23100         100   0.011770367    0.011770367    0.0088631275   0.0010809683 
+     23200         100   0.0099747299   0.0099747299   0.0076787282   0.00049951509
+     23300         100   0.01031026     0.01031026     0.0079525195   0.00064873732
+     23400         100   0.0096104307   0.0096104307   0.0072783079   0.00045628129
+     23500         100   0.0092403444   0.0092403444   0.0069910691   0.00055860189
+     23600         100   0.0087158451   0.0087158451   0.0064234628   0.00042327506
+     23700         100   0.0076095087   0.0076095087   0.005524052    0.00040612722
+     23800         100   0.0073236191   0.0073236191   0.0054016138   0.0002882358 
+     23900         100   0.0076690517   0.0076690517   0.0054567733   0.000294478  
+     24000         100   0.0068826778   0.0068826778   0.0049332647   0.00025128376
+     24100         100   0.006293019    0.006293019    0.0046682205   0.00029832544
+     24200         100   0.005767467    0.005767467    0.0043594373   0.00026379963
+     24300         100   0.005071854    0.005071854    0.0038348196   0.00026374758
+     24400         100   0.0051487759   0.0051487759   0.0038569741   0.00047689032
+     24500         100   0.0045914722   0.0045914722   0.0034370386   0.00026920355
+     24600         100   0.0042661938   0.0042661938   0.0031638249   0.00023704631
+     24700         100   0.0038978286   0.0038978286   0.0028913869   0.00029112049
+     24800         100   0.0033993745   0.0033993745   0.0025640275   0.00054348397
+     24900         100   0.0030064864   0.0030064864   0.0022631158   0.00016374877
+     25000         100   0.0030540972   0.0030540972   0.0022935172   0.00012379035
+Loop time of 0.531538 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 4063677.790 tau/day, 9406.662 timesteps/s, 940.666 katom-step/s
+96.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00017249 | 0.0025494  | 0.0063723  |   5.1 |  0.48
+Neigh   | 0.00078415 | 0.0017788  | 0.0029816  |   2.4 |  0.33
+Comm    | 0.0024926  | 0.0084554  | 0.015551   |   6.0 |  1.59
+Output  | 0.35621    | 0.40519    | 0.46627    |   6.6 | 76.23
+Modify  | 0.00052416 | 0.018236   | 0.04055    |  13.3 |  3.43
+Other   |            | 0.09532    |            |       | 17.93
+
+Nlocal:             25 ave          57 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:           5.25 ave          13 max           0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:          38.75 ave          96 max           0 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 155
+Ave neighs/atom = 1.55
+Neighbor list builds = 183
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/gransurf/log.1Jul24.tribox.gran.surf.g++.1

@@ -0,0 +1,515 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+molecule        tris surf.tribox
+Read molecule template tris:
+LAMMPS data file for tri box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  24 triangles
+fix             20 all surface/local tris
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.31 | 7.31 | 7.31 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0029137134 
+       200          54   0.65485258     1.1967995      0.5882574      0.0043383984 
+       300          54   0.70118095     1.2814686      0.62987441     0.0046453238 
+       400          54   0.45057814     0.82347039     0.41172861     0.0030892546 
+       500          54   0.42112344     0.76963938     0.38709352     0.0065941015 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.37166521     0.51325196     0.26472957     0.0046580242 
+       700          88   0.41372338     0.57133229     0.29476966     0.0052995687 
+       800          88   0.456666       0.630634       0.32751956     0.0052868185 
+       900          88   0.39272615     0.54233611     0.28819808     0.0054685106 
+      1000          88   0.35151938     0.48543152     0.26491902     0.0075844126 
+      1100          88   0.34254338     0.47303609     0.2578388      0.0058365561 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.32173809     0.40053109     0.2195167      0.009133967  
+      1300         123   0.34297407     0.42696772     0.23049402     0.0064335441 
+      1400         123   0.29833429     0.37139575     0.20331799     0.0078377048 
+      1500         123   0.26892843     0.33478846     0.18670497     0.0068237101 
+      1600         123   0.24084602     0.29982872     0.16693769     0.0058533752 
+      1700         124   0.16657955     0.20696247     0.12302494     0.0070405476 
+      1800         124   0.10384588     0.12902064     0.086085999    0.0026199715 
+      1900         124   0.065080172    0.080857183    0.059672578    0.0039751399 
+      2000         124   0.05183749     0.064404155    0.04642994     0.0020956381 
+      2100         124   0.045454362    0.056473601    0.038678168    0.0021869997 
+      2200         124   0.040260905    0.050021124    0.034386815    0.0040428451 
+      2300         124   0.017599393    0.021865913    0.017659764    0.0033409468 
+      2400         124   0.017871721    0.022204259    0.016705944    0.0035685432 
+      2500         124   0.010140453    0.012598745    0.01022206     0.0012285049 
+      2600         124   0.0087985586   0.010931542    0.0087284393   0.0012843554 
+      2700         124   0.007517666    0.0093401305   0.00718198     0.0014841823 
+      2800         124   0.0062773841   0.0077991742   0.0059012301   0.0013324193 
+      2900         124   0.0038811224   0.0048220006   0.0039901849   0.0012740179 
+      3000         124   0.0040758656   0.0050639543   0.003890039    0.001333468  
+      3100         124   0.0020497159   0.0025466167   0.0022373889   0.0012963602 
+      3200         124   0.0019596496   0.0024347162   0.0021331337   0.0011575952 
+      3300         124   0.001619509    0.0020121172   0.0017930305   0.0011065531 
+      3400         124   0.0013352687   0.0016589702   0.0014836146   0.0013075216 
+      3500         124   0.0011048269   0.0013726637   0.0012547142   0.0016936826 
+      3600         124   0.00089868347  0.0011165461   0.0010379824   0.0013037755 
+      3700         124   0.00079538563  0.00098820638  0.0008953041   0.0011379267 
+      3800         124   0.00072591855  0.0009018988   0.00083210028  0.0014623234 
+      3900         124   0.00059200429  0.00073552048  0.00068255735  0.0011062713 
+      4000         124   0.00048509163  0.0006026896   0.00057581131  0.0011359453 
+      4100         124   0.00039281562  0.00048804365  0.00046290412  0.001112345  
+      4200         124   0.00033127035  0.00041157831  0.00040230271  0.0011101349 
+      4300         124   0.00025217556  0.00031330904  0.00033013679  0.001220284  
+      4400         124   0.00021998869  0.00027331928  0.00029069852  0.0010876934 
+      4500         124   0.0002012981   0.00025009764  0.00026845495  0.0011165366 
+      4600         124   0.00019974132  0.00024816346  0.00026538627  0.001112397  
+      4700         124   0.00018344096  0.0002279115   0.00024939407  0.0011208162 
+      4800         124   0.00017967553  0.00022323323  0.00024517143  0.0011139226 
+      4900         124   0.00015575257  0.00019351076  0.000215109    0.0011122181 
+      5000         124   0.00013945209  0.00017325866  0.00019787988  0.0011571915 
+Loop time of 0.317507 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6803005.318 tau/day, 15747.697 timesteps/s, 1.953 Matom-step/s
+94.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.049124   | 0.049124   | 0.049124   |   0.0 | 15.47
+Neigh   | 0.012461   | 0.012461   | 0.012461   |   0.0 |  3.92
+Comm    | 0.00036472 | 0.00036472 | 0.00036472 |   0.0 |  0.11
+Output  | 0.25022    | 0.25022    | 0.25022    |   0.0 | 78.81
+Modify  | 0.0041121  | 0.0041121  | 0.0041121  |   0.0 |  1.30
+Other   |            | 0.001224   |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.437 | 8.437 | 8.437 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00013945209  0.00017325866  0.00019787988  0.0011523447 
+      5100         124   5.2504023      0.15308533     0.087279574    0.082413806  
+      5200         124   5.2659596      0.17241407     0.099384862    0.083118924  
+      5300         124   5.2712193      0.17894892     0.099626237    0.084288849  
+      5400         124   5.2787049      0.18824913     0.10219206     0.081763058  
+      5500         124   5.2864544      0.19787729     0.10492289     0.082100381  
+      5600         124   5.2939393      0.20717681     0.10842003     0.081936074  
+      5700         124   5.3020913      0.21730504     0.11309658     0.083096264  
+      5800         124   5.3089934      0.22588036     0.11657282     0.083472698  
+      5900         124   5.3147183      0.23299307     0.12000481     0.083337683  
+      6000         124   5.3241216      0.24467603     0.12524512     0.083312456  
+      6100         124   5.3345453      0.25762669     0.13135815     0.083666287  
+      6200         124   5.3357153      0.25908032     0.13185776     0.083855111  
+      6300         124   5.3417298      0.26655284     0.13521844     0.084511512  
+      6400         124   5.3461733      0.27207356     0.1375877      0.08445019   
+      6500         124   5.3491551      0.27577827     0.13949034     0.084694686  
+      6600         124   5.3520289      0.27934872     0.14134154     0.084403705  
+      6700         124   5.355841       0.28408494     0.1435925      0.08479568   
+      6800         124   5.3608822      0.29034823     0.14636154     0.084796891  
+      6900         124   5.3641064      0.29435404     0.14822031     0.084636583  
+      7000         124   5.3664936      0.29731999     0.14957082     0.084681424  
+      7100         124   5.370434       0.30221567     0.15171915     0.084744017  
+      7200         124   5.3716029      0.30366789     0.15224159     0.085599998  
+      7300         124   5.3719337      0.30407894     0.15239181     0.085265794  
+      7400         124   5.3717886      0.30389862     0.15228125     0.085048862  
+      7500         124   5.3729819      0.30538125     0.15302965     0.085513236  
+      7600         124   5.3736409      0.30619992     0.15346603     0.085126903  
+      7700         124   5.3734973      0.30602161     0.15326715     0.085870776  
+      7800         124   5.3742065      0.3069027      0.1536922      0.085152121  
+      7900         124   5.3752637      0.30821621     0.15439789     0.085476609  
+      8000         124   5.3773145      0.31076416     0.15559007     0.085791749  
+      8100         124   5.3777123      0.31125838     0.15591462     0.08531435   
+      8200         124   5.3775898      0.31110617     0.1558302      0.085752338  
+      8300         124   5.3775553      0.31106337     0.15562475     0.086300437  
+      8400         124   5.3799091      0.31398779     0.1570463      0.085260347  
+      8500         124   5.3799831      0.31407966     0.15713064     0.085373576  
+      8600         124   5.380017       0.31412181     0.15720523     0.085342084  
+      8700         124   5.3799686      0.31406171     0.15721123     0.086223474  
+      8800         124   5.3813565      0.31578601     0.15798281     0.085392543  
+      8900         124   5.3815941      0.31608116     0.15818243     0.085482019  
+      9000         124   5.3815651      0.31604517     0.15821916     0.085538444  
+      9100         124   5.3816424      0.31614127     0.15829616     0.085684184  
+      9200         124   5.3815641      0.3160439      0.15831347     0.08526896   
+      9300         124   5.3811199      0.31549204     0.15801464     0.085848004  
+      9400         124   5.382478       0.31717943     0.15882722     0.086145692  
+      9500         124   5.3830353      0.31787185     0.15915683     0.085450771  
+      9600         124   5.3831332      0.31799341     0.15923155     0.085416324  
+      9700         124   5.3832948      0.31819419     0.15935762     0.085387545  
+      9800         124   5.3840779      0.31916711     0.15975721     0.08560667   
+      9900         124   5.3842171      0.31934012     0.159845       0.085547365  
+     10000         124   5.3862101      0.32181619     0.160876       0.085414766  
+Loop time of 0.353055 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6118026.711 tau/day, 14162.099 timesteps/s, 1.756 Matom-step/s
+96.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.070537   | 0.070537   | 0.070537   |   0.0 | 19.98
+Neigh   | 0.019928   | 0.019928   | 0.019928   |   0.0 |  5.64
+Comm    | 0.00042487 | 0.00042487 | 0.00042487 |   0.0 |  0.12
+Output  | 0.2524     | 0.2524     | 0.2524     |   0.0 | 71.49
+Modify  | 0.0083924  | 0.0083924  | 0.0083924  |   0.0 |  2.38
+Other   |            | 0.001368   |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 315
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.562 | 7.562 | 7.562 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.25902279     0.32181619     0.160876       0.0066564852 
+     10100         124   0.078320106    0.097306799    0.060539222    0.007805448  
+     10200         124   0.055004387    0.068338784    0.052320677    0.0026461505 
+     10300         124   0.050013703    0.062138237    0.049351053    0.0027137895 
+     10400         124   0.043870518    0.054505795    0.044683006    0.0021708086 
+     10500         124   0.036776691    0.045692252    0.037872077    0.0025876629 
+     10600         124   0.030001621    0.037274742    0.032601767    0.0035817232 
+     10700         124   0.026098209    0.032425048    0.029320364    0.0019774985 
+     10800         124   0.024452388    0.03038024     0.028518503    0.0034548101 
+     10900         124   0.020787653    0.025827084    0.025880067    0.0023865627 
+     11000         124   0.018283729    0.022716148    0.024283842    0.0024791255 
+     11100         124   0.016795448    0.020867072    0.023416045    0.0016336875 
+     11200         124   0.014930262    0.01854972     0.021981853    0.0015505118 
+     11300         124   0.014012114    0.017408991    0.021130907    0.0017795037 
+     11400         124   0.013562682    0.016850605    0.020502505    0.0025724773 
+     11500         124   0.012884492    0.016008005    0.01991195     0.0015754014 
+     11600         124   0.011953832    0.014851731    0.018960689    0.0020007622 
+     11700         124   0.011836339    0.014705755    0.019435427    0.0016103993 
+     11800         124   0.011037076    0.013712731    0.018997693    0.0019540971 
+     11900         124   0.010932107    0.013582315    0.019072917    0.00147549   
+     12000         124   0.01099415     0.013659399    0.018695305    0.0016223256 
+     12100         124   0.010704976    0.013300121    0.018841965    0.0015737757 
+     12200         124   0.010244691    0.012728253    0.018984857    0.0023548154 
+     12300         124   0.0097078529   0.012061272    0.018340321    0.0020279841 
+     12400         124   0.0093873799   0.011663108    0.018058176    0.0017085133 
+     12500         124   0.0091864665   0.011413489    0.016617566    0.0029005125 
+     12600         124   0.0093721201   0.011644149    0.01659216     0.001843826  
+     12700         124   0.0085867868   0.010668432    0.01610889     0.0027852908 
+     12800         124   0.0080688661   0.010024955    0.016412496    0.0035052823 
+     12900         124   0.0070827536   0.0087997848   0.014807272    0.0023574294 
+     13000         124   0.0062582856   0.0077754457   0.01480373     0.0027340736 
+     13100         124   0.0057725257   0.0071719259   0.015062076    0.002487901  
+     13200         124   0.0052896823   0.0065720295   0.0154416      0.0015994582 
+     13300         124   0.0057364664   0.0071271249   0.015700129    0.0015451013 
+     13400         124   0.0062684466   0.00778807     0.016185631    0.0018109382 
+     13500         124   0.0057823202   0.0071840947   0.015642287    0.0023353672 
+     13600         124   0.0054893444   0.0068200946   0.015197387    0.0020769185 
+     13700         124   0.0052411899   0.0065117814   0.014647838    0.0018125771 
+     13800         124   0.0048067514   0.0059720245   0.014583902    0.0020513529 
+     13900         124   0.0050435734   0.0062662579   0.015595068    0.0014699579 
+     14000         124   0.0049460152   0.0061450492   0.015965634    0.001392331  
+     14100         124   0.0046219442   0.0057424155   0.015663384    0.0014890253 
+     14200         124   0.0048184995   0.0059866206   0.015290196    0.0017217599 
+     14300         124   0.0049531756   0.0061539454   0.015631133    0.0020820646 
+     14400         124   0.004608077    0.0057251866   0.01512022     0.0015346016 
+     14500         124   0.0044909079   0.0055796129   0.015032761    0.0016169354 
+     14600         124   0.0044307569   0.0055048797   0.015259724    0.0019791575 
+     14700         124   0.0042209282   0.0052441835   0.015206142    0.001634029  
+     14800         124   0.004931427    0.0061269245   0.015351353    0.0020991125 
+     14900         124   0.0043513432   0.0054062142   0.014367168    0.0022798395 
+     15000         124   0.0044465482   0.0055244993   0.014488799    0.0027071352 
+Loop time of 0.328479 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6575768.459 tau/day, 15221.686 timesteps/s, 1.887 Matom-step/s
+96.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.058012   | 0.058012   | 0.058012   |   0.0 | 17.66
+Neigh   | 0.0059592  | 0.0059592  | 0.0059592  |   0.0 |  1.81
+Comm    | 0.00031492 | 0.00031492 | 0.00031492 |   0.0 |  0.10
+Output  | 0.25848    | 0.25848    | 0.25848    |   0.0 | 78.69
+Modify  | 0.0044353  | 0.0044353  | 0.0044353  |   0.0 |  1.35
+Other   |            | 0.001276   |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 94
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.437 | 8.437 | 8.437 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0044465482   0.0055244993   0.014488799    0.002682599  
+     15100         124   5.2439101      0.14501926     0.089393313    0.0861951    
+     15200         124   5.2871886      0.19878957     0.11689814     0.087629076  
+     15300         124   5.3269872      0.24823627     0.14065555     0.084448851  
+     15400         124   5.318405       0.23757348     0.13557872     0.08579496   
+     15500         124   5.322977       0.24325395     0.1367731      0.084332501  
+     15600         124   5.3387157      0.26280804     0.14469795     0.091920302  
+     15700         124   5.3468954      0.27297066     0.14714255     0.092776597  
+     15800         124   5.3787123      0.31250075     0.16363996     0.091882707  
+     15900         124   5.4124578      0.354427       0.18222961     0.090476713  
+     16000         124   5.4095058      0.35075937     0.17808408     0.090347477  
+     16100         124   5.4027965      0.34242354     0.1735999      0.091782107  
+     16200         124   5.4022601      0.34175711     0.17335141     0.094848056  
+     16300         124   5.4045444      0.34459525     0.17424728     0.093070457  
+     16400         124   5.4101141      0.35151512     0.17740527     0.091595086  
+     16500         124   5.4083344      0.34930396     0.1760425      0.09403337   
+     16600         124   5.4016713      0.34102557     0.17264803     0.091701205  
+     16700         124   5.3964053      0.33448303     0.16952454     0.097389495  
+     16800         124   5.4155708      0.35829473     0.18177437     0.092539674  
+     16900         124   5.428106       0.37386868     0.18956572     0.095082983  
+     17000         124   5.4113572      0.35305963     0.17951019     0.093172207  
+     17100         124   5.4017206      0.34108687     0.17437504     0.090773913  
+     17200         124   5.4156275      0.35836508     0.18539559     0.084238411  
+     17300         124   5.4009849      0.34017277     0.17748735     0.092123575  
+     17400         124   5.4017142      0.34107897     0.18110554     0.08358144   
+     17500         124   5.438404       0.38666317     0.20673435     0.08724577   
+     17600         124   5.5085355      0.47379629     0.25395237     0.085044882  
+     17700         124   5.573336       0.55430604     0.29833936     0.086018483  
+     17800         124   5.6428243      0.64063997     0.34884622     0.091543453  
+     17900         124   5.6885972      0.69750927     0.38081471     0.090348055  
+     18000         124   5.7119205      0.72648671     0.3965357      0.095583224  
+     18100         124   5.6590292      0.66077326     0.36523218     0.088750557  
+     18200         124   5.5763862      0.55809563     0.31550553     0.096656501  
+     18300         124   5.5505114      0.52594811     0.2987063      0.093142352  
+     18400         124   5.5205731      0.48875209     0.2808444      0.087905083  
+     18500         124   5.4892953      0.44989178     0.26426272     0.088670881  
+     18600         124   5.4222293      0.36656731     0.22263438     0.087525924  
+     18700         124   5.4048793      0.34501133     0.2146507      0.086965023  
+     18800         124   5.4091495      0.35031672     0.21471813     0.088080028  
+     18900         124   5.4055995      0.34590616     0.21031053     0.085893342  
+     19000         124   5.3793845      0.31333589     0.19319866     0.091199294  
+     19100         124   5.3860486      0.32161564     0.19859682     0.089765384  
+     19200         124   5.3927702      0.32996663     0.20403509     0.088705875  
+     19300         124   5.3971859      0.33545284     0.20175175     0.095973464  
+     19400         124   5.3788197      0.3126342      0.18579792     0.089895991  
+     19500         124   5.3885341      0.32470369     0.18948024     0.08907407   
+     19600         124   5.4101398      0.35154706     0.19813337     0.091175233  
+     19700         124   5.4044673      0.34449937     0.1920192      0.088240134  
+     19800         124   5.4173446      0.36049849     0.19933328     0.088942313  
+     19900         124   5.4076506      0.34845443     0.1927872      0.088186985  
+     20000         124   5.3956924      0.33359732     0.18569985     0.086310528  
+Loop time of 0.373054 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5790041.220 tau/day, 13402.873 timesteps/s, 1.662 Matom-step/s
+94.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.062905   | 0.062905   | 0.062905   |   0.0 | 16.86
+Neigh   | 0.0304     | 0.0304     | 0.0304     |   0.0 |  8.15
+Comm    | 0.0004825  | 0.0004825  | 0.0004825  |   0.0 |  0.13
+Output  | 0.26963    | 0.26963    | 0.26963    |   0.0 | 72.28
+Modify  | 0.00823    | 0.00823    | 0.00823    |   0.0 |  2.21
+Other   |            | 0.001409   |            |       |  0.38
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 440
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.562 | 7.562 | 7.562 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         124   0.26850516     0.33359732     0.18569985    -0.00058742278
+     20100         124   0.067549955    0.083925702    0.063062899    0.0045374238 
+     20200         124   0.066580568    0.082721312    0.059638881    0.0046773578 
+     20300         124   0.07628847     0.094782644    0.062421657    0.0046893994 
+     20400         124   0.052816991    0.06562111     0.047589744    0.0028448251 
+     20500         124   0.055535483    0.068998631    0.048552669    0.0030160754 
+     20600         124   0.057734099    0.071730244    0.048245877    0.0055952666 
+     20700         124   0.025276846    0.031404566    0.029056653    0.0010557897 
+     20800         124   0.027799744    0.034539076    0.028465929    0.0054351904 
+     20900         124   0.027298566    0.033916401    0.027639247    0.0040270655 
+     21000         124   0.024024164    0.029848203    0.024340109    0.0021868639 
+     21100         124   0.024987535    0.031045119    0.025194034    0.0031461768 
+     21200         124   0.022012372    0.027348704    0.023163575    0.0043315251 
+     21300         124   0.022655698    0.028147988    0.023878073    0.0020061516 
+     21400         124   0.021143161    0.026268775    0.022847649    0.0040014299 
+     21500         124   0.014709587    0.018275548    0.016687241    0.0023850643 
+     21600         124   0.015706963    0.019514711    0.017385202    0.0032947123 
+     21700         124   0.013349261    0.016585446    0.015935512    0.0031959548 
+     21800         124   0.014581152    0.018115977    0.016568563    0.0037723007 
+     21900         124   0.014163143    0.017596633    0.016786239    0.0026785551 
+     22000         124   0.016104454    0.020008564    0.018204239    0.0023406746 
+     22100         124   0.01339249     0.016639155    0.016215231    0.001863965  
+     22200         124   0.013630138    0.016934414    0.015604721    0.0028389532 
+     22300         124   0.014166961    0.017601376    0.015759254    0.0028485515 
+     22400         124   0.011839829    0.014710091    0.014221942    0.0017289255 
+     22500         124   0.013154489    0.016343456    0.015344524    0.002604136  
+     22600         124   0.01184812     0.014720391    0.014245522    0.0033590472 
+     22700         124   0.011433291    0.014204998    0.013639711    0.0033184417 
+     22800         124   0.012475296    0.01549961     0.014280851    0.0019255869 
+     22900         124   0.011013166    0.013683025    0.012635318    0.0022642412 
+     23000         124   0.011272729    0.014005511    0.012664054    0.0031554482 
+     23100         124   0.011308641    0.01405013     0.01269757     0.0012325204 
+     23200         124   0.010130039    0.012585807    0.012040563    0.0031495614 
+     23300         124   0.01068914     0.013280447    0.012068167    0.0030504659 
+     23400         124   0.0088509283   0.010996608    0.010081312    0.0011009871 
+     23500         124   0.0086960335   0.010804163    0.0098039166   0.0016850167 
+     23600         124   0.0099572186   0.01237109     0.010813937    0.0029185027 
+     23700         124   0.0099220344   0.012327376    0.01019147     0.0041517151 
+     23800         124   0.0074584766   0.0092665922   0.00878623     0.0033529004 
+     23900         124   0.0073723023   0.0091595271   0.0091933559   0.0011381908 
+     24000         124   0.0085493541   0.010621925    0.0099793177   0.0023747349 
+     24100         124   0.0067898783   0.0084359094   0.0089497737   0.0034141299 
+     24200         124   0.0060281758   0.0074895517   0.0087835149   0.0010072857 
+     24300         124   0.0060915949   0.0075683452   0.0085728503   0.0018651179 
+     24400         124   0.0064602712   0.0080263976   0.0089108593   0.00097753256
+     24500         124   0.0069832749   0.00867619     0.0096009113   0.0012080821 
+     24600         124   0.006177616    0.0076752198   0.0086417752   0.0017792353 
+     24700         124   0.0052226061   0.0064886924   0.0082196264   0.0011437075 
+     24800         124   0.0051375444   0.0063830098   0.0083830573   0.0026277208 
+     24900         124   0.0037569854   0.0046677698   0.0072102729   0.0017298399 
+     25000         124   0.0039418359   0.0048974325   0.0073209218   0.0011140053 
+Loop time of 0.332906 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6488317.108 tau/day, 15019.253 timesteps/s, 1.862 Matom-step/s
+94.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.055597   | 0.055597   | 0.055597   |   0.0 | 16.70
+Neigh   | 0.0121     | 0.0121     | 0.0121     |   0.0 |  3.63
+Comm    | 0.00035777 | 0.00035777 | 0.00035777 |   0.0 |  0.11
+Output  | 0.25919    | 0.25919    | 0.25919    |   0.0 | 77.86
+Modify  | 0.0043494  | 0.0043494  | 0.0043494  |   0.0 |  1.31
+Other   |            | 0.00131    |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 197
+Dangerous builds = 0
+
+Total wall time: 0:00:01

examples/gransurf/log.1Jul24.tribox.gran.surf.g++.4

@@ -0,0 +1,516 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+molecule        tris surf.tribox
+Read molecule template tris:
+LAMMPS data file for tri box
+  1 molecules
+  0 fragments
+  0 atoms with max type 0
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+  24 triangles
+fix             20 all surface/local tris
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.337 | 7.338 | 7.342 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0029137134 
+       200          54   0.65485258     1.1967995      0.5882574      0.0043383984 
+       300          54   0.70118095     1.2814686      0.62987441     0.0046453238 
+       400          54   0.45057814     0.82347039     0.41172861     0.0030892546 
+       500          54   0.42112344     0.76963938     0.38709352     0.0065941015 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.37166521     0.51325196     0.26472957     0.0046580242 
+       700          88   0.41372338     0.57133229     0.29476966     0.0052995687 
+       800          88   0.456666       0.630634       0.32751956     0.0052868185 
+       900          88   0.39272615     0.54233611     0.28819808     0.0054685106 
+      1000          88   0.35151938     0.48543152     0.26491902     0.0075844126 
+      1100          88   0.34254338     0.47303609     0.2578388      0.0058365561 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.32173809     0.40053109     0.2195167      0.009133967  
+      1300         123   0.34297407     0.42696772     0.23049402     0.0064335441 
+      1400         123   0.29833429     0.37139575     0.20331799     0.0078377048 
+      1500         123   0.26892843     0.33478846     0.18670497     0.0068237101 
+      1600         123   0.24084602     0.29982872     0.16693769     0.0058533752 
+      1700         124   0.16657955     0.20696247     0.12302494     0.0070405476 
+      1800         124   0.10384588     0.12902064     0.086085999    0.0026199715 
+      1900         124   0.065080172    0.080857183    0.059672578    0.0039751399 
+      2000         124   0.05183749     0.064404155    0.04642994     0.0020956381 
+      2100         124   0.045454362    0.056473601    0.038678168    0.0021870001 
+      2200         124   0.040260905    0.050021124    0.034386815    0.0040428451 
+      2300         124   0.017599392    0.021865912    0.017659763    0.0033409473 
+      2400         124   0.017871716    0.022204254    0.016705941    0.0035685425 
+      2500         124   0.010140454    0.012598746    0.010222061    0.0012285151 
+      2600         124   0.0087985619   0.010931547    0.0087284273   0.0012844023 
+      2700         124   0.007517679    0.0093401466   0.0071819965   0.0014841812 
+      2800         124   0.0062774012   0.0077991955   0.0059012475   0.0013323867 
+      2900         124   0.0038811559   0.0048220422   0.0039902314   0.0012740306 
+      3000         124   0.0040746036   0.0050623863   0.0038882236   0.0013782794 
+      3100         124   0.0020498002   0.0025467215   0.0022365676   0.00121108   
+      3200         124   0.0019550482   0.0024289992   0.0021292434   0.0011484714 
+      3300         124   0.0016148199   0.0020062914   0.001787787    0.0010893844 
+      3400         124   0.0013434329   0.0016691136   0.0014690989   0.001325505  
+      3500         124   0.0010971454   0.00136312     0.0012496656   0.0014062237 
+      3600         124   0.00089514745  0.0011121529   0.0010349137   0.0013004041 
+      3700         124   0.00079220295  0.00098425215  0.00089325412  0.0013154029 
+      3800         124   0.00072319138  0.0008985105   0.00082122483  0.0010962257 
+      3900         124   0.00059169918  0.00073514141  0.0006832875   0.0011623171 
+      4000         124   0.00049184916  0.00061108533  0.00058188229  0.0012411181 
+      4100         124   0.00040680153  0.00050542008  0.00047870676  0.0011629016 
+      4200         124   0.00030588217  0.00038003543  0.00038246927  0.001099663  
+      4300         124   0.00026922252  0.00033448858  0.00034959953  0.0011174124 
+      4400         124   0.00022239176  0.00027630491  0.0002971948   0.0011072118 
+      4500         124   0.00020343817  0.00025275651  0.00027474732  0.0011125161 
+      4600         124   0.00020212818  0.00025112896  0.00027242474  0.0011191532 
+      4700         124   0.00018351448  0.00022800283  0.00025264863  0.0011176353 
+      4800         124   0.00018007372  0.00022372795  0.00024857425  0.0011156418 
+      4900         124   0.00015459176  0.00019206855  0.00021711531  0.0011174087 
+      5000         124   0.00013814109  0.00017162984  0.00019806357  0.0011476165 
+Loop time of 0.38831 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5562573.007 tau/day, 12876.326 timesteps/s, 1.597 Matom-step/s
+90.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0018869  | 0.015601   | 0.030549   |  10.9 |  4.02
+Neigh   | 0.0018269  | 0.0044514  | 0.0069007  |   3.6 |  1.15
+Comm    | 0.06426    | 0.079269   | 0.093176   |   4.8 | 20.41
+Output  | 0.18739    | 0.22364    | 0.27884    |   7.6 | 57.59
+Modify  | 0.0013862  | 0.002664   | 0.0040784  |   2.3 |  0.69
+Other   |            | 0.06269    |            |       | 16.14
+
+Nlocal:             31 ave          55 max           6 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         118 max          69 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00013814109  0.00017162984  0.00019806357  0.0011393845 
+      5100         124   5.2497489      0.15227351     0.086950224    0.083018439  
+      5200         124   5.2667941      0.17345097     0.10004552     0.081933375  
+      5300         124   5.2702467      0.17774046     0.098721846    0.081858913  
+      5400         124   5.2810321      0.1911405      0.10284442     0.081908237  
+      5500         124   5.2869181      0.19845342     0.10520589     0.082475287  
+      5600         124   5.2903829      0.20275822     0.1062221      0.082060713  
+      5700         124   5.2972601      0.21130259     0.11014372     0.082904363  
+      5800         124   5.3133933      0.23134691     0.11895223     0.082638221  
+      5900         124   5.321421       0.24132073     0.12341367     0.08367512   
+      6000         124   5.3311871      0.25345436     0.1289868      0.08585114   
+      6100         124   5.3397784      0.26412833     0.13380251     0.083860885  
+      6200         124   5.3440946      0.26949097     0.13630397     0.084294896  
+      6300         124   5.3490438      0.27563994     0.13938066     0.084316514  
+      6400         124   5.3513948      0.27856086     0.14088282     0.084355453  
+      6500         124   5.3532922      0.28091822     0.14197211     0.084169662  
+      6600         124   5.3554267      0.28357014     0.14325168     0.084261645  
+      6700         124   5.3570557      0.2855941      0.14433458     0.084810743  
+      6800         124   5.360655       0.29006592     0.14636096     0.084297488  
+      6900         124   5.3655245      0.29611592     0.14908452     0.085243202  
+      7000         124   5.3671924      0.29818814     0.14990767     0.085406818  
+      7100         124   5.3695979      0.30117682     0.15113793     0.084784596  
+      7200         124   5.3704771      0.30226917     0.15173765     0.085669989  
+      7300         124   5.3706216      0.3024487      0.15180341     0.084798844  
+      7400         124   5.373135       0.30557147     0.15321903     0.085809531  
+      7500         124   5.377898       0.31148903     0.15599818     0.085242244  
+      7600         124   5.3787889      0.31259599     0.15641937     0.085326973  
+      7700         124   5.3793411      0.31328199     0.15676105     0.084950755  
+      7800         124   5.3803167      0.31449408     0.15736738     0.085202699  
+      7900         124   5.3797837      0.31383196     0.15704082     0.085404305  
+      8000         124   5.378568       0.31232146     0.15632737     0.084957387  
+      8100         124   5.3790479      0.31291774     0.15667738     0.08504012   
+      8200         124   5.3804618      0.3146744      0.15746304     0.085394022  
+      8300         124   5.381518       0.31598663     0.1580058      0.085647397  
+      8400         124   5.3814854      0.31594618     0.15794776     0.085483103  
+      8500         124   5.3828149      0.31759794     0.15875289     0.085382128  
+      8600         124   5.3832577      0.31814807     0.15901813     0.085100022  
+      8700         124   5.3838083      0.31883219     0.1593819      0.085126575  
+      8800         124   5.3842963      0.31943849     0.15972799     0.085207191  
+      8900         124   5.3846809      0.31991635     0.15992599     0.085139646  
+      9000         124   5.3850037      0.32031738     0.16014788     0.085113229  
+      9100         124   5.3849209      0.32021445     0.16009856     0.086008106  
+      9200         124   5.3851663      0.32051942     0.16025838     0.085113861  
+      9300         124   5.3847882      0.32004969     0.16001717     0.085571311  
+      9400         124   5.3845996      0.31981535     0.15990007     0.085364837  
+      9500         124   5.3847067      0.31994844     0.15998733     0.085299109  
+      9600         124   5.3849015      0.32019038     0.1601311      0.085276233  
+      9700         124   5.3850083      0.32032313     0.16021695     0.08525484   
+      9800         124   5.3852855      0.32066753     0.16041712     0.085313652  
+      9900         124   5.3850371      0.3203589      0.16026849     0.085310954  
+     10000         124   5.3851839      0.32054133     0.16038666     0.085302918  
+Loop time of 0.416211 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5189670.286 tau/day, 12013.126 timesteps/s, 1.490 Matom-step/s
+91.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0051455  | 0.025429   | 0.046204   |  12.6 |  6.11
+Neigh   | 0.002146   | 0.0071526  | 0.012427   |   5.9 |  1.72
+Comm    | 0.075914   | 0.099171   | 0.12133    |   7.0 | 23.83
+Output  | 0.1817     | 0.21488    | 0.2715     |   8.0 | 51.63
+Modify  | 0.0028369  | 0.0042822  | 0.0059817  |   2.2 |  1.03
+Other   |            | 0.0653     |            |       | 15.69
+
+Nlocal:             31 ave          59 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:             93 ave         116 max          65 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 316
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.714 | 7.726 | 7.737 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.25799668     0.32054133     0.16038666     0.011646419  
+     10100         124   0.08324921     0.10343084     0.062335766    0.0036624752 
+     10200         124   0.055901794    0.069453744    0.049832932    0.0033728561 
+     10300         124   0.044027763    0.054701161    0.04185265     0.0026179937 
+     10400         124   0.033039084    0.04104856     0.033838053    0.0042759187 
+     10500         124   0.027910031    0.034676099    0.03032615     0.0035478069 
+     10600         124   0.023950341    0.029756484    0.027453511    0.0021787132 
+     10700         124   0.019265986    0.023936529    0.024195141    0.0021075014 
+     10800         124   0.01792324     0.022268268    0.02351488     0.0024045592 
+     10900         124   0.016637573    0.020670924    0.022003538    0.0034529435 
+     11000         124   0.01309629     0.016271149    0.019359267    0.0017153891 
+     11100         124   0.011683446    0.014515797    0.018854763    0.0026746409 
+     11200         124   0.010761235    0.013370019    0.018196576    0.0029245106 
+     11300         124   0.010091525    0.012537955    0.017818489    0.0015293592 
+     11400         124   0.0096257383   0.011959251    0.017339573    0.001738964  
+     11500         124   0.0090651598   0.011262774    0.017333091    0.001572136  
+     11600         124   0.0083289641   0.010348107    0.016333003    0.0017025439 
+     11700         124   0.0082472994   0.010246645    0.015938935    0.0014901853 
+     11800         124   0.0084807765   0.010536722    0.016623711    0.0014242448 
+     11900         124   0.007712302    0.009581951    0.016222065    0.001508232  
+     12000         124   0.0075675523   0.0094021104   0.016169534    0.0014905945 
+     12100         124   0.0079750147   0.0099083516   0.015149716    0.0018322585 
+     12200         124   0.0078458496   0.0097478738   0.015374706    0.0015492292 
+     12300         124   0.0067921053   0.0084386763   0.013486857    0.0029067448 
+     12400         124   0.0068508251   0.0085116312   0.014323963    0.0022197074 
+     12500         124   0.0066111171   0.0082138122   0.014731325    0.0019302025 
+     12600         124   0.0064707353   0.0080393984   0.014543367    0.0016587329 
+     12700         124   0.0063923274   0.0079419826   0.014294803    0.0021257946 
+     12800         124   0.0065672963   0.0081593681   0.014584204    0.0021816878 
+     12900         124   0.0059726164   0.0074205234   0.013858993    0.001530472  
+     13000         124   0.0058214195   0.0072326727   0.014246373    0.0022339129 
+     13100         124   0.0059612276   0.0074063737   0.015124804    0.0017832816 
+     13200         124   0.0054078557   0.006718851    0.014415419    0.0015478062 
+     13300         124   0.0050729677   0.0063027781   0.014411303    0.0034332889 
+     13400         124   0.0050627437   0.0062900755   0.014575044    0.0018503274 
+     13500         124   0.0046199761   0.0057399703   0.015232064    0.0015707131 
+     13600         124   0.0044802838   0.0055664132   0.015492936    0.0013436939 
+     13700         124   0.0039229012   0.0048739075   0.014834411    0.0015775897 
+     13800         124   0.0038496507   0.0047828994   0.014358939    0.0018648078 
+     13900         124   0.0038836627   0.0048251567   0.015268416    0.0016609027 
+     14000         124   0.0039681599   0.0049301381   0.015565026    0.0015819215 
+     14100         124   0.0038047814   0.0047271526   0.013834942    0.0026360599 
+     14200         124   0.0039663433   0.004927881    0.014740545    0.0017718033 
+     14300         124   0.0042501525   0.0052804925   0.015931298    0.0015106704 
+     14400         124   0.0043324422   0.0053827312   0.014699138    0.0017419936 
+     14500         124   0.0051700329   0.0064233742   0.014614744    0.0017929379 
+     14600         124   0.0051378715   0.006383416    0.015531966    0.001759876  
+     14700         124   0.0043671736   0.0054258823   0.014990071    0.0014624588 
+     14800         124   0.0045615958   0.0056674372   0.014632879    0.001980479  
+     14900         124   0.0043120591   0.0053574067   0.014648647    0.0017081314 
+     15000         124   0.0040016693   0.004971771    0.015227426    0.0014981674 
+Loop time of 0.383969 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5625453.581 tau/day, 13021.883 timesteps/s, 1.615 Matom-step/s
+93.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00068953 | 0.018285   | 0.03985    |  13.2 |  4.76
+Neigh   | 0.00065387 | 0.0021284  | 0.0039605  |   3.2 |  0.55
+Comm    | 0.067454   | 0.088442   | 0.1049     |   5.6 | 23.03
+Output  | 0.17852    | 0.21163    | 0.26515    |   7.5 | 55.12
+Modify  | 0.00076231 | 0.0021966  | 0.0037187  |   3.0 |  0.57
+Other   |            | 0.06129    |            |       | 15.96
+
+Nlocal:             31 ave          54 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         116 max          70 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 88
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0040016693   0.004971771    0.015227426    0.0015086634 
+     15100         124   5.2391455      0.13909965     0.086544429    0.084187091  
+     15200         124   5.2856213      0.19684224     0.11745683     0.083186315  
+     15300         124   5.3131372      0.23102865     0.13493822     0.08605977   
+     15400         124   5.312441       0.23016376     0.13361748     0.085326393  
+     15500         124   5.3238039      0.24428132     0.13748765     0.083860323  
+     15600         124   5.3492159      0.27585379     0.15195482     0.090509109  
+     15700         124   5.3793259      0.31326319     0.16813451     0.094842314  
+     15800         124   5.3836817      0.31867484     0.17028976     0.089989699  
+     15900         124   5.3796952      0.31372196     0.16538847     0.094472961  
+     16000         124   5.4115814      0.3533382      0.18150785     0.091208354  
+     16100         124   5.3936511      0.33106115     0.17088137     0.093629945  
+     16200         124   5.3957378      0.33365363     0.17021817     0.099559486  
+     16300         124   5.4107263      0.35227575     0.17833256     0.097418633  
+     16400         124   5.4157911      0.35856834     0.18023194     0.094902693  
+     16500         124   5.4104949      0.35198831     0.17667749     0.098565938  
+     16600         124   5.409282       0.35048133     0.17592806     0.096041734  
+     16700         124   5.413877       0.35619023     0.1787891      0.092627526  
+     16800         124   5.41431        0.35672824     0.1791246      0.094118962  
+     16900         124   5.4131542      0.35529219     0.17881883     0.092708811  
+     17000         124   5.4141932      0.35658307     0.1798655      0.090520504  
+     17100         124   5.4220385      0.3663303      0.18519617     0.089222997  
+     17200         124   5.4046579      0.34473618     0.17738138     0.094492682  
+     17300         124   5.4056346      0.34594968     0.17932898     0.087067848  
+     17400         124   5.4625758      0.4166948      0.21590291     0.087573329  
+     17500         124   5.5101683      0.47582488     0.24840276     0.086186395  
+     17600         124   5.5878392      0.5723251      0.29850268     0.08748419   
+     17700         124   5.6772998      0.6834732      0.36153625     0.091782683  
+     17800         124   5.7649819      0.79241148     0.41944601     0.091955533  
+     17900         124   5.6293884      0.6239469      0.34262388     0.092222925  
+     18000         124   5.5993719      0.58665365     0.3202341      0.092041421  
+     18100         124   5.5929165      0.57863332     0.31757988     0.089752868  
+     18200         124   5.5194314      0.48733363     0.27391729     0.088604294  
+     18300         124   5.5558601      0.53259351     0.29860433     0.087707501  
+     18400         124   5.5243479      0.49344201     0.28138274     0.091109598  
+     18500         124   5.4712545      0.4274775      0.24899279     0.085579285  
+     18600         124   5.4614746      0.41532663     0.24277803     0.093560936  
+     18700         124   5.4335266      0.38060339     0.22486156     0.092857653  
+     18800         124   5.4062944      0.34676949     0.20805012     0.085928259  
+     18900         124   5.3680383      0.29923911     0.18445379     0.09139396   
+     19000         124   5.3612247      0.29077372     0.17705414     0.091152733  
+     19100         124   5.3657774      0.29643016     0.18163087     0.088533894  
+     19200         124   5.3753017      0.30826343     0.18731953     0.090708858  
+     19300         124   5.3788607      0.31268517     0.18511328     0.091858903  
+     19400         124   5.3753079      0.30827114     0.18028529     0.094270307  
+     19500         124   5.3793587      0.31330386     0.17822453     0.09479624   
+     19600         124   5.3794279      0.31338982     0.17247606     0.088668785  
+     19700         124   5.3883131      0.3244291      0.17733088     0.089605063  
+     19800         124   5.3862701      0.32189078     0.17600167     0.087391973  
+     19900         124   5.3627176      0.2926286      0.15793773     0.087196402  
+     20000         124   5.371666       0.30374625     0.16190487     0.08799023   
+Loop time of 0.44519 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 4851866.281 tau/day, 11231.172 timesteps/s, 1.393 Matom-step/s
+94.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.010338   | 0.023654   | 0.039387   |   8.5 |  5.31
+Neigh   | 0.0046555  | 0.0104     | 0.019115   |   5.9 |  2.34
+Comm    | 0.082693   | 0.10525    | 0.12179    |   5.2 | 23.64
+Output  | 0.1884     | 0.23171    | 0.29261    |   8.5 | 52.05
+Modify  | 0.0033946  | 0.0047351  | 0.0067516  |   2.1 |  1.06
+Other   |            | 0.06944    |            |       | 15.60
+
+Nlocal:             31 ave          73 max           6 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:             93 ave         118 max          51 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 429
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.737 | 7.746 | 7.773 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         124   0.24447869     0.30374625     0.16190487    -0.013113207  
+     20100         124   0.058472851    0.072648087    0.051241435    0.0027199931 
+     20200         124   0.052338782    0.065026972    0.04463957     0.0049181017 
+     20300         124   0.059032454    0.073343352    0.046997972    0.0036432387 
+     20400         124   0.041540522    0.051610952    0.034851914    0.0080319941 
+     20500         124   0.034253651    0.042557567    0.030035232    0.0085785376 
+     20600         124   0.027090159    0.03365747     0.025218135    0.0056701536 
+     20700         124   0.023080903    0.028676274    0.022777714    0.0021487926 
+     20800         124   0.024811993    0.030827022    0.023644112    0.0031902401 
+     20900         124   0.02296688     0.028534608    0.022697322    0.0052975401 
+     21000         124   0.024959299    0.031010038    0.023833456    0.0049399041 
+     21100         124   0.024560924    0.030515087    0.022657931    0.0034176814 
+     21200         124   0.025331395    0.031472339    0.023297144    0.0051700371 
+     21300         124   0.023119592    0.028724342    0.021901117    0.0028542595 
+     21400         124   0.021068783    0.026176367    0.02024999     0.0066313423 
+     21500         124   0.019958716    0.024797192    0.020021151    0.0054394297 
+     21600         124   0.021501915    0.026714501    0.021044833    0.003139584  
+     21700         124   0.022663473    0.028157649    0.021375039    0.0047077744 
+     21800         124   0.017783349    0.022094464    0.018460952    0.0024408478 
+     21900         124   0.017441008    0.021669131    0.017976927    0.004236632  
+     22000         124   0.016834232    0.020915258    0.017867023    0.0032297246 
+     22100         124   0.016852641    0.02093813     0.017823693    0.0031993194 
+     22200         124   0.017260002    0.021444245    0.018617101    0.001645186  
+     22300         124   0.016279285    0.020225778    0.017759307    0.0048239099 
+     22400         124   0.013098535    0.016273937    0.014976085    0.0030481479 
+     22500         124   0.01253107     0.015568906    0.014821105    0.002818037  
+     22600         124   0.013231925    0.016439664    0.014841942    0.0061556104 
+     22700         124   0.010622794    0.013198017    0.013335312    0.0032549657 
+     22800         124   0.012715053    0.01579749     0.01437656     0.0017626703 
+     22900         124   0.01207747     0.015005341    0.013708244    0.0018658438 
+     23000         124   0.010825905    0.013450367    0.01253289     0.0024262171 
+     23100         124   0.010506745    0.013053834    0.012086254    0.0013807784 
+     23200         124   0.010816779    0.013439028    0.012089622    0.0020534022 
+     23300         124   0.010541511    0.013097028    0.012162291    0.0020542813 
+     23400         124   0.0094678491   0.011763085    0.011404012    0.0011667903 
+     23500         124   0.0083682956   0.010396973    0.010273685    0.0025941956 
+     23600         124   0.0076879289   0.0095516693   0.0099437632   0.0014724848 
+     23700         124   0.0087792045   0.010907496    0.010802224    0.0017158203 
+     23800         124   0.0070944354   0.0088142985   0.010176751    0.0030678737 
+     23900         124   0.0073071217   0.0090785451   0.010067352    0.0021355515 
+     24000         124   0.007092681    0.0088121188   0.0093578983   0.0037224355 
+     24100         124   0.0061240788   0.0076087039   0.0088323652   0.00075591612
+     24200         124   0.0060997333   0.0075784566   0.0089160306   0.00074919945
+     24300         124   0.0074369071   0.0092397936   0.0098936814   0.0016742568 
+     24400         124   0.0055774041   0.0069295021   0.0089788427   0.0010941333 
+     24500         124   0.0054891817   0.0068198925   0.0089585787   0.0010201513 
+     24600         124   0.0052665503   0.0065432898   0.0085195212   0.0027803091 
+     24700         124   0.0052229505   0.0064891203   0.0083245915   0.0032441386 
+     24800         124   0.0045885549   0.0057009318   0.0077639469   0.0021437792 
+     24900         124   0.0048155198   0.0059829185   0.0082794836   0.0013531019 
+     25000         124   0.0051022231   0.0063391257   0.0084155114   0.0026277693 
+Loop time of 0.41091 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5256626.239 tau/day, 12168.116 timesteps/s, 1.509 Matom-step/s
+90.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00076076 | 0.01794    | 0.039603   |  13.0 |  4.37
+Neigh   | 0.00072049 | 0.0035802  | 0.0068029  |   4.6 |  0.87
+Comm    | 0.075306   | 0.095878   | 0.11196    |   5.3 | 23.33
+Output  | 0.17491    | 0.2221     | 0.28159    |   8.6 | 54.05
+Modify  | 0.00088166 | 0.0023597  | 0.0040721  |   3.0 |  0.57
+Other   |            | 0.06906    |            |       | 16.81
+
+Nlocal:             31 ave          58 max           5 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         119 max          66 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 149
+Dangerous builds = 0
+
+Total wall time: 0:00:02

examples/gransurf/log.1Jul24.tribox.gran.surf.stl.g++.1

@@ -0,0 +1,508 @@
+LAMMPS (27 Jun 2024)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+fix             20 all surface/local surf.tribox.stl
+Reading STL object STL version of surf.tribox from text file surf.tribox.stl
+set             type 1 type 2
+Setting atom values ...
+  24 settings made for type
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.31 | 7.31 | 7.31 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0029137134 
+       200          54   0.65485258     1.1967995      0.5882574      0.0043383984 
+       300          54   0.70118095     1.2814686      0.62987441     0.0046453238 
+       400          54   0.45057814     0.82347039     0.41172861     0.0030892546 
+       500          54   0.42112344     0.76963938     0.38709352     0.0065941015 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.37166521     0.51325196     0.26472957     0.0046580242 
+       700          88   0.41372338     0.57133229     0.29476966     0.0052995687 
+       800          88   0.456666       0.630634       0.32751956     0.0052868185 
+       900          88   0.39272615     0.54233611     0.28819808     0.0054685106 
+      1000          88   0.35151938     0.48543152     0.26491902     0.0075844126 
+      1100          88   0.34254338     0.47303609     0.2578388      0.0058365561 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.32173809     0.40053109     0.2195167      0.009133967  
+      1300         123   0.34297407     0.42696772     0.23049402     0.0064335441 
+      1400         123   0.29833429     0.37139575     0.20331799     0.0078377048 
+      1500         123   0.26892843     0.33478846     0.18670497     0.0068237101 
+      1600         123   0.24084602     0.29982872     0.16693769     0.0058533752 
+      1700         124   0.16657955     0.20696247     0.12302494     0.0070405476 
+      1800         124   0.10384588     0.12902064     0.086085999    0.0026199715 
+      1900         124   0.065080172    0.080857183    0.059672578    0.0039751399 
+      2000         124   0.05183749     0.064404155    0.04642994     0.0020956381 
+      2100         124   0.045454362    0.056473601    0.038678168    0.0021869997 
+      2200         124   0.040260905    0.050021124    0.034386815    0.0040428451 
+      2300         124   0.017599393    0.021865913    0.017659764    0.0033409468 
+      2400         124   0.017871721    0.022204259    0.016705944    0.0035685432 
+      2500         124   0.010140453    0.012598745    0.01022206     0.0012285049 
+      2600         124   0.0087985586   0.010931542    0.0087284393   0.0012843554 
+      2700         124   0.007517666    0.0093401305   0.00718198     0.0014841823 
+      2800         124   0.0062773841   0.0077991742   0.0059012301   0.0013324193 
+      2900         124   0.0038811224   0.0048220006   0.0039901849   0.0012740179 
+      3000         124   0.0040758656   0.0050639543   0.003890039    0.001333468  
+      3100         124   0.0020497159   0.0025466167   0.0022373889   0.0012963602 
+      3200         124   0.0019596496   0.0024347162   0.0021331337   0.0011575952 
+      3300         124   0.001619509    0.0020121172   0.0017930305   0.0011065531 
+      3400         124   0.0013352687   0.0016589702   0.0014836146   0.0013075216 
+      3500         124   0.0011048269   0.0013726637   0.0012547142   0.0016936826 
+      3600         124   0.00089868347  0.0011165461   0.0010379824   0.0013037755 
+      3700         124   0.00079538563  0.00098820638  0.0008953041   0.0011379267 
+      3800         124   0.00072591855  0.0009018988   0.00083210028  0.0014623234 
+      3900         124   0.00059200429  0.00073552048  0.00068255735  0.0011062713 
+      4000         124   0.00048509163  0.0006026896   0.00057581131  0.0011359453 
+      4100         124   0.00039281562  0.00048804365  0.00046290412  0.001112345  
+      4200         124   0.00033127035  0.00041157831  0.00040230271  0.0011101349 
+      4300         124   0.00025217556  0.00031330904  0.00033013679  0.001220284  
+      4400         124   0.00021998869  0.00027331928  0.00029069852  0.0010876934 
+      4500         124   0.0002012981   0.00025009764  0.00026845495  0.0011165366 
+      4600         124   0.00019974132  0.00024816346  0.00026538627  0.001112397  
+      4700         124   0.00018344096  0.0002279115   0.00024939407  0.0011208162 
+      4800         124   0.00017967553  0.00022323323  0.00024517143  0.0011139226 
+      4900         124   0.00015575257  0.00019351076  0.000215109    0.0011122181 
+      5000         124   0.00013945209  0.00017325866  0.00019787988  0.0011571915 
+Loop time of 0.329081 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6563731.175 tau/day, 15193.822 timesteps/s, 1.884 Matom-step/s
+89.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.050766   | 0.050766   | 0.050766   |   0.0 | 15.43
+Neigh   | 0.012777   | 0.012777   | 0.012777   |   0.0 |  3.88
+Comm    | 0.00039761 | 0.00039761 | 0.00039761 |   0.0 |  0.12
+Output  | 0.25886    | 0.25886    | 0.25886    |   0.0 | 78.66
+Modify  | 0.0049275  | 0.0049275  | 0.0049275  |   0.0 |  1.50
+Other   |            | 0.00135    |            |       |  0.41
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.437 | 8.437 | 8.437 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00013945209  0.00017325866  0.00019787988  0.0011523447 
+      5100         124   5.2504023      0.15308533     0.087279574    0.082413806  
+      5200         124   5.2659596      0.17241407     0.099384862    0.083118924  
+      5300         124   5.2712193      0.17894892     0.099626237    0.084288849  
+      5400         124   5.2787049      0.18824913     0.10219206     0.081763058  
+      5500         124   5.2864544      0.19787729     0.10492289     0.082100381  
+      5600         124   5.2939393      0.20717681     0.10842003     0.081936074  
+      5700         124   5.3020913      0.21730504     0.11309658     0.083096264  
+      5800         124   5.3089934      0.22588036     0.11657282     0.083472698  
+      5900         124   5.3147183      0.23299307     0.12000481     0.083337683  
+      6000         124   5.3241216      0.24467603     0.12524512     0.083312456  
+      6100         124   5.3345453      0.25762669     0.13135815     0.083666287  
+      6200         124   5.3357153      0.25908032     0.13185776     0.083855111  
+      6300         124   5.3417298      0.26655284     0.13521844     0.084511512  
+      6400         124   5.3461733      0.27207356     0.1375877      0.08445019   
+      6500         124   5.3491551      0.27577827     0.13949034     0.084694686  
+      6600         124   5.3520289      0.27934872     0.14134154     0.084403705  
+      6700         124   5.355841       0.28408494     0.1435925      0.08479568   
+      6800         124   5.3608822      0.29034823     0.14636154     0.084796891  
+      6900         124   5.3641064      0.29435404     0.14822031     0.084636583  
+      7000         124   5.3664936      0.29731999     0.14957082     0.084681424  
+      7100         124   5.370434       0.30221567     0.15171915     0.084744017  
+      7200         124   5.3716029      0.30366789     0.15224159     0.085599998  
+      7300         124   5.3719337      0.30407894     0.15239181     0.085265794  
+      7400         124   5.3717886      0.30389862     0.15228125     0.085048862  
+      7500         124   5.3729819      0.30538125     0.15302965     0.085513236  
+      7600         124   5.3736409      0.30619992     0.15346603     0.085126903  
+      7700         124   5.3734973      0.30602161     0.15326715     0.085870776  
+      7800         124   5.3742065      0.3069027      0.1536922      0.085152121  
+      7900         124   5.3752637      0.30821621     0.15439789     0.085476609  
+      8000         124   5.3773145      0.31076416     0.15559007     0.085791749  
+      8100         124   5.3777123      0.31125838     0.15591462     0.08531435   
+      8200         124   5.3775898      0.31110617     0.1558302      0.085752338  
+      8300         124   5.3775553      0.31106337     0.15562475     0.086300437  
+      8400         124   5.3799091      0.31398779     0.1570463      0.085260347  
+      8500         124   5.3799831      0.31407966     0.15713064     0.085373576  
+      8600         124   5.380017       0.31412181     0.15720523     0.085342084  
+      8700         124   5.3799686      0.31406171     0.15721123     0.086223474  
+      8800         124   5.3813565      0.31578601     0.15798281     0.085392543  
+      8900         124   5.3815941      0.31608116     0.15818243     0.085482019  
+      9000         124   5.3815651      0.31604517     0.15821916     0.085538444  
+      9100         124   5.3816424      0.31614127     0.15829616     0.085684184  
+      9200         124   5.3815641      0.3160439      0.15831347     0.08526896   
+      9300         124   5.3811199      0.31549204     0.15801464     0.085848004  
+      9400         124   5.382478       0.31717943     0.15882722     0.086145692  
+      9500         124   5.3830353      0.31787185     0.15915683     0.085450771  
+      9600         124   5.3831332      0.31799341     0.15923155     0.085416324  
+      9700         124   5.3832948      0.31819419     0.15935762     0.085387545  
+      9800         124   5.3840779      0.31916711     0.15975721     0.08560667   
+      9900         124   5.3842171      0.31934012     0.159845       0.085547365  
+     10000         124   5.3862101      0.32181619     0.160876       0.085414766  
+Loop time of 0.367085 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5884203.709 tau/day, 13620.842 timesteps/s, 1.689 Matom-step/s
+97.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.073918   | 0.073918   | 0.073918   |   0.0 | 20.14
+Neigh   | 0.020255   | 0.020255   | 0.020255   |   0.0 |  5.52
+Comm    | 0.00045729 | 0.00045729 | 0.00045729 |   0.0 |  0.12
+Output  | 0.26157    | 0.26157    | 0.26157    |   0.0 | 71.26
+Modify  | 0.0093671  | 0.0093671  | 0.0093671  |   0.0 |  2.55
+Other   |            | 0.001516   |            |       |  0.41
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 315
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.562 | 7.562 | 7.562 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.25902279     0.32181619     0.160876       0.0066564852 
+     10100         124   0.078320106    0.097306799    0.060539222    0.007805448  
+     10200         124   0.055004387    0.068338784    0.052320677    0.0026461505 
+     10300         124   0.050013703    0.062138237    0.049351053    0.0027137895 
+     10400         124   0.043870518    0.054505795    0.044683006    0.0021708086 
+     10500         124   0.036776691    0.045692252    0.037872077    0.0025876629 
+     10600         124   0.030001621    0.037274742    0.032601767    0.0035817232 
+     10700         124   0.026098209    0.032425048    0.029320364    0.0019774985 
+     10800         124   0.024452388    0.03038024     0.028518503    0.0034548101 
+     10900         124   0.020787653    0.025827084    0.025880067    0.0023865627 
+     11000         124   0.018283729    0.022716148    0.024283842    0.0024791255 
+     11100         124   0.016795448    0.020867072    0.023416045    0.0016336875 
+     11200         124   0.014930262    0.01854972     0.021981853    0.0015505118 
+     11300         124   0.014012114    0.017408991    0.021130907    0.0017795037 
+     11400         124   0.013562682    0.016850605    0.020502505    0.0025724773 
+     11500         124   0.012884492    0.016008005    0.01991195     0.0015754014 
+     11600         124   0.011953832    0.014851731    0.018960689    0.0020007622 
+     11700         124   0.011836339    0.014705755    0.019435427    0.0016103993 
+     11800         124   0.011037076    0.013712731    0.018997693    0.0019540971 
+     11900         124   0.010932107    0.013582315    0.019072917    0.00147549   
+     12000         124   0.01099415     0.013659399    0.018695305    0.0016223256 
+     12100         124   0.010704976    0.013300121    0.018841965    0.0015737757 
+     12200         124   0.010244691    0.012728253    0.018984857    0.0023548154 
+     12300         124   0.0097078529   0.012061272    0.018340321    0.0020279841 
+     12400         124   0.0093873799   0.011663108    0.018058176    0.0017085133 
+     12500         124   0.0091864665   0.011413489    0.016617566    0.0029005125 
+     12600         124   0.0093721201   0.011644149    0.01659216     0.001843826  
+     12700         124   0.0085867868   0.010668432    0.01610889     0.0027852908 
+     12800         124   0.0080688661   0.010024955    0.016412496    0.0035052823 
+     12900         124   0.0070827536   0.0087997848   0.014807272    0.0023574294 
+     13000         124   0.0062582856   0.0077754457   0.01480373     0.0027340736 
+     13100         124   0.0057725257   0.0071719259   0.015062076    0.002487901  
+     13200         124   0.0052896823   0.0065720295   0.0154416      0.0015994582 
+     13300         124   0.0057364664   0.0071271249   0.015700129    0.0015451013 
+     13400         124   0.0062684466   0.00778807     0.016185631    0.0018109382 
+     13500         124   0.0057823202   0.0071840947   0.015642287    0.0023353672 
+     13600         124   0.0054893444   0.0068200946   0.015197387    0.0020769185 
+     13700         124   0.0052411899   0.0065117814   0.014647838    0.0018125771 
+     13800         124   0.0048067514   0.0059720245   0.014583902    0.0020513529 
+     13900         124   0.0050435734   0.0062662579   0.015595068    0.0014699579 
+     14000         124   0.0049460152   0.0061450492   0.015965634    0.001392331  
+     14100         124   0.0046219442   0.0057424155   0.015663384    0.0014890253 
+     14200         124   0.0048184995   0.0059866206   0.015290196    0.0017217599 
+     14300         124   0.0049531756   0.0061539454   0.015631133    0.0020820646 
+     14400         124   0.004608077    0.0057251866   0.01512022     0.0015346016 
+     14500         124   0.0044909079   0.0055796129   0.015032761    0.0016169354 
+     14600         124   0.0044307569   0.0055048797   0.015259724    0.0019791575 
+     14700         124   0.0042209282   0.0052441835   0.015206142    0.001634029  
+     14800         124   0.004931427    0.0061269245   0.015351353    0.0020991125 
+     14900         124   0.0043513432   0.0054062142   0.014367168    0.0022798395 
+     15000         124   0.0044465482   0.0055244993   0.014488799    0.0027071352 
+Loop time of 0.342327 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6309759.447 tau/day, 14605.925 timesteps/s, 1.811 Matom-step/s
+92.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.059911   | 0.059911   | 0.059911   |   0.0 | 17.50
+Neigh   | 0.0061776  | 0.0061776  | 0.0061776  |   0.0 |  1.80
+Comm    | 0.00033294 | 0.00033294 | 0.00033294 |   0.0 |  0.10
+Output  | 0.26919    | 0.26919    | 0.26919    |   0.0 | 78.64
+Modify  | 0.0053451  | 0.0053451  | 0.0053451  |   0.0 |  1.56
+Other   |            | 0.001367   |            |       |  0.40
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 94
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.437 | 8.437 | 8.437 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0044465482   0.0055244993   0.014488799    0.002682599  
+     15100         124   5.2439101      0.14501926     0.089393313    0.0861951    
+     15200         124   5.2871886      0.19878957     0.11689814     0.087629076  
+     15300         124   5.3269872      0.24823627     0.14065555     0.084448851  
+     15400         124   5.318405       0.23757348     0.13557872     0.08579496   
+     15500         124   5.322977       0.24325395     0.1367731      0.084332501  
+     15600         124   5.3387157      0.26280804     0.14469795     0.091920302  
+     15700         124   5.3468954      0.27297066     0.14714255     0.092776597  
+     15800         124   5.3787123      0.31250075     0.16363996     0.091882707  
+     15900         124   5.4124578      0.354427       0.18222961     0.090476713  
+     16000         124   5.4095058      0.35075937     0.17808408     0.090347477  
+     16100         124   5.4027965      0.34242354     0.1735999      0.091782107  
+     16200         124   5.4022601      0.34175711     0.17335141     0.094848056  
+     16300         124   5.4045444      0.34459525     0.17424728     0.093070457  
+     16400         124   5.4101141      0.35151512     0.17740527     0.091595086  
+     16500         124   5.4083344      0.34930396     0.1760425      0.09403337   
+     16600         124   5.4016713      0.34102557     0.17264803     0.091701205  
+     16700         124   5.3964053      0.33448303     0.16952454     0.097389495  
+     16800         124   5.4155708      0.35829473     0.18177437     0.092539674  
+     16900         124   5.428106       0.37386868     0.18956572     0.095082983  
+     17000         124   5.4113572      0.35305963     0.17951019     0.093172207  
+     17100         124   5.4017206      0.34108687     0.17437504     0.090773913  
+     17200         124   5.4156275      0.35836508     0.18539559     0.084238411  
+     17300         124   5.4009849      0.34017277     0.17748735     0.092123575  
+     17400         124   5.4017142      0.34107897     0.18110554     0.08358144   
+     17500         124   5.438404       0.38666317     0.20673435     0.08724577   
+     17600         124   5.5085355      0.47379629     0.25395237     0.085044882  
+     17700         124   5.573336       0.55430604     0.29833936     0.086018483  
+     17800         124   5.6428243      0.64063997     0.34884622     0.091543453  
+     17900         124   5.6885972      0.69750927     0.38081471     0.090348055  
+     18000         124   5.7119205      0.72648671     0.3965357      0.095583224  
+     18100         124   5.6590292      0.66077326     0.36523218     0.088750557  
+     18200         124   5.5763862      0.55809563     0.31550553     0.096656501  
+     18300         124   5.5505114      0.52594811     0.2987063      0.093142352  
+     18400         124   5.5205731      0.48875209     0.2808444      0.087905083  
+     18500         124   5.4892953      0.44989178     0.26426272     0.088670881  
+     18600         124   5.4222293      0.36656731     0.22263438     0.087525924  
+     18700         124   5.4048793      0.34501133     0.2146507      0.086965023  
+     18800         124   5.4091495      0.35031672     0.21471813     0.088080028  
+     18900         124   5.4055995      0.34590616     0.21031053     0.085893342  
+     19000         124   5.3793845      0.31333589     0.19319866     0.091199294  
+     19100         124   5.3860486      0.32161564     0.19859682     0.089765384  
+     19200         124   5.3927702      0.32996663     0.20403509     0.088705875  
+     19300         124   5.3971859      0.33545284     0.20175175     0.095973464  
+     19400         124   5.3788197      0.3126342      0.18579792     0.089895991  
+     19500         124   5.3885341      0.32470369     0.18948024     0.08907407   
+     19600         124   5.4101398      0.35154706     0.19813337     0.091175233  
+     19700         124   5.4044673      0.34449937     0.1920192      0.088240134  
+     19800         124   5.4173446      0.36049849     0.19933328     0.088942313  
+     19900         124   5.4076506      0.34845443     0.1927872      0.088186985  
+     20000         124   5.3956924      0.33359732     0.18569985     0.086310528  
+Loop time of 0.389106 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 5551183.841 tau/day, 12849.963 timesteps/s, 1.593 Matom-step/s
+95.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.065646   | 0.065646   | 0.065646   |   0.0 | 16.87
+Neigh   | 0.031221   | 0.031221   | 0.031221   |   0.0 |  8.02
+Comm    | 0.00053075 | 0.00053075 | 0.00053075 |   0.0 |  0.14
+Output  | 0.28071    | 0.28071    | 0.28071    |   0.0 | 72.14
+Modify  | 0.0094938  | 0.0094938  | 0.0094938  |   0.0 |  2.44
+Other   |            | 0.001506   |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 440
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.562 | 7.562 | 7.562 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         124   0.26850516     0.33359732     0.18569985    -0.00058742278
+     20100         124   0.067549955    0.083925702    0.063062899    0.0045374238 
+     20200         124   0.066580568    0.082721312    0.059638881    0.0046773578 
+     20300         124   0.07628847     0.094782644    0.062421657    0.0046893994 
+     20400         124   0.052816991    0.06562111     0.047589744    0.0028448251 
+     20500         124   0.055535483    0.068998631    0.048552669    0.0030160754 
+     20600         124   0.057734099    0.071730244    0.048245877    0.0055952666 
+     20700         124   0.025276846    0.031404566    0.029056653    0.0010557897 
+     20800         124   0.027799744    0.034539076    0.028465929    0.0054351904 
+     20900         124   0.027298566    0.033916401    0.027639247    0.0040270655 
+     21000         124   0.024024164    0.029848203    0.024340109    0.0021868639 
+     21100         124   0.024987535    0.031045119    0.025194034    0.0031461768 
+     21200         124   0.022012372    0.027348704    0.023163575    0.0043315251 
+     21300         124   0.022655698    0.028147988    0.023878073    0.0020061516 
+     21400         124   0.021143161    0.026268775    0.022847649    0.0040014299 
+     21500         124   0.014709587    0.018275548    0.016687241    0.0023850643 
+     21600         124   0.015706963    0.019514711    0.017385202    0.0032947123 
+     21700         124   0.013349261    0.016585446    0.015935512    0.0031959548 
+     21800         124   0.014581152    0.018115977    0.016568563    0.0037723007 
+     21900         124   0.014163143    0.017596633    0.016786239    0.0026785551 
+     22000         124   0.016104454    0.020008564    0.018204239    0.0023406746 
+     22100         124   0.01339249     0.016639155    0.016215231    0.001863965  
+     22200         124   0.013630138    0.016934414    0.015604721    0.0028389532 
+     22300         124   0.014166961    0.017601376    0.015759254    0.0028485515 
+     22400         124   0.011839829    0.014710091    0.014221942    0.0017289255 
+     22500         124   0.013154489    0.016343456    0.015344524    0.002604136  
+     22600         124   0.01184812     0.014720391    0.014245522    0.0033590472 
+     22700         124   0.011433291    0.014204998    0.013639711    0.0033184417 
+     22800         124   0.012475296    0.01549961     0.014280851    0.0019255869 
+     22900         124   0.011013166    0.013683025    0.012635318    0.0022642412 
+     23000         124   0.011272729    0.014005511    0.012664054    0.0031554482 
+     23100         124   0.011308641    0.01405013     0.01269757     0.0012325204 
+     23200         124   0.010130039    0.012585807    0.012040563    0.0031495614 
+     23300         124   0.01068914     0.013280447    0.012068167    0.0030504659 
+     23400         124   0.0088509283   0.010996608    0.010081312    0.0011009871 
+     23500         124   0.0086960335   0.010804163    0.0098039166   0.0016850167 
+     23600         124   0.0099572186   0.01237109     0.010813937    0.0029185027 
+     23700         124   0.0099220344   0.012327376    0.01019147     0.0041517151 
+     23800         124   0.0074584766   0.0092665922   0.00878623     0.0033529004 
+     23900         124   0.0073723023   0.0091595271   0.0091933559   0.0011381908 
+     24000         124   0.0085493541   0.010621925    0.0099793177   0.0023747349 
+     24100         124   0.0067898783   0.0084359094   0.0089497737   0.0034141299 
+     24200         124   0.0060281758   0.0074895517   0.0087835149   0.0010072857 
+     24300         124   0.0060915949   0.0075683452   0.0085728503   0.0018651179 
+     24400         124   0.0064602712   0.0080263976   0.0089108593   0.00097753256
+     24500         124   0.0069832749   0.00867619     0.0096009113   0.0012080821 
+     24600         124   0.006177616    0.0076752198   0.0086417752   0.0017792353 
+     24700         124   0.0052226061   0.0064886924   0.0082196264   0.0011437075 
+     24800         124   0.0051375444   0.0063830098   0.0083830573   0.0026277208 
+     24900         124   0.0037569854   0.0046677698   0.0072102729   0.0017298399 
+     25000         124   0.0039418359   0.0048974325   0.0073209218   0.0011140053 
+Loop time of 0.347029 on 1 procs for 5000 steps with 124 atoms
+
+Performance: 6224261.616 tau/day, 14408.013 timesteps/s, 1.787 Matom-step/s
+94.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.057242   | 0.057242   | 0.057242   |   0.0 | 16.49
+Neigh   | 0.01241    | 0.01241    | 0.01241    |   0.0 |  3.58
+Comm    | 0.00038529 | 0.00038529 | 0.00038529 |   0.0 |  0.11
+Output  | 0.27021    | 0.27021    | 0.27021    |   0.0 | 77.86
+Modify  | 0.0054264  | 0.0054264  | 0.0054264  |   0.0 |  1.56
+Other   |            | 0.001359   |            |       |  0.39
+
+Nlocal:            124 ave         124 max         124 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:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 197
+Dangerous builds = 0
+
+Total wall time: 0:00:01

examples/gransurf/log.1Jul24.tribox.gran.surf.stl.g++.4

@@ -0,0 +1,509 @@
+LAMMPS (27 Jun 2024)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
+# pouring spheres into box made of triangles
+
+units		lj
+atom_style	tri
+atom_modify     map array
+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
+
+fix             20 all surface/local surf.tribox.stl
+Reading STL object STL version of surf.tribox from text file surf.tribox.stl
+set             type 1 type 2
+Setting atom values ...
+  24 settings made for type
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1                 tri/gran/hooke 4000.0 NULL 100.0 50.0 0.5 1
+pair_coeff	1 1 gran/hooke
+pair_coeff	1 2 tri/gran/hooke
+pair_coeff	2 2 none
+
+group           sphere type 1
+0 atoms in group sphere
+group           tri type 2
+24 atoms in group tri
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+#displace_atoms  all rotate 0 0 0 0 0 1 45
+
+fix             2 sphere nve/sphere
+fix		3 sphere gravity 1.0 vector 0 0 -1
+#fix             4 sphere viscous 0.2
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins sphere pour 100 1 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 sphere temp
+compute_modify  1 dynamic yes
+
+compute         2 sphere temp/sphere
+compute_modify  2 dynamic yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic yes
+
+dump		2 all image 100 tmp.image.*.ppm type type 		zoom 1.4 adiam 1.0 tri type 2 0.2
+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 = 7.1245553
+  ghost atom cutoff = 7.1245553
+  binsize = 3.5622777, bins = 6 6 6
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair gran/hooke, perpetual, skip trim from (3)
+      attributes: half, newton on, size, cut 1.3, off2on
+      pair build: skip/trim/size/off2on
+      stencil: none
+      bin: none
+  (2) pair tri/gran/hooke, perpetual, skip from (3)
+      attributes: half, newton on, size, onesided, off2on
+      pair build: skip/size/off2on/oneside
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton off, size
+      pair build: half/size/bin/atomonly/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.337 | 7.338 | 7.342 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0          24   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       100          54   0.43980579     0.803783       0.39507978     0.0029137134 
+       200          54   0.65485258     1.1967995      0.5882574      0.0043383984 
+       300          54   0.70118095     1.2814686      0.62987441     0.0046453238 
+       400          54   0.45057814     0.82347039     0.41172861     0.0030892546 
+       500          54   0.42112344     0.76963938     0.38709352     0.0065941015 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+       600          88   0.37166521     0.51325196     0.26472957     0.0046580242 
+       700          88   0.41372338     0.57133229     0.29476966     0.0052995687 
+       800          88   0.456666       0.630634       0.32751956     0.0052868185 
+       900          88   0.39272615     0.54233611     0.28819808     0.0054685106 
+      1000          88   0.35151938     0.48543152     0.26491902     0.0075844126 
+      1100          88   0.34254338     0.47303609     0.2578388      0.0058365561 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:683)
+      1200         123   0.32173809     0.40053109     0.2195167      0.009133967  
+      1300         123   0.34297407     0.42696772     0.23049402     0.0064335441 
+      1400         123   0.29833429     0.37139575     0.20331799     0.0078377048 
+      1500         123   0.26892843     0.33478846     0.18670497     0.0068237101 
+      1600         123   0.24084602     0.29982872     0.16693769     0.0058533752 
+      1700         124   0.16657955     0.20696247     0.12302494     0.0070405476 
+      1800         124   0.10384588     0.12902064     0.086085999    0.0026199715 
+      1900         124   0.065080172    0.080857183    0.059672578    0.0039751399 
+      2000         124   0.05183749     0.064404155    0.04642994     0.0020956381 
+      2100         124   0.045454362    0.056473601    0.038678168    0.0021870001 
+      2200         124   0.040260905    0.050021124    0.034386815    0.0040428451 
+      2300         124   0.017599392    0.021865912    0.017659763    0.0033409473 
+      2400         124   0.017871716    0.022204254    0.016705941    0.0035685425 
+      2500         124   0.010140454    0.012598746    0.010222061    0.0012285151 
+      2600         124   0.0087985619   0.010931547    0.0087284273   0.0012844023 
+      2700         124   0.007517679    0.0093401466   0.0071819965   0.0014841812 
+      2800         124   0.0062774012   0.0077991955   0.0059012475   0.0013323867 
+      2900         124   0.0038811559   0.0048220422   0.0039902314   0.0012740306 
+      3000         124   0.0040746036   0.0050623863   0.0038882236   0.0013782794 
+      3100         124   0.0020498002   0.0025467215   0.0022365676   0.00121108   
+      3200         124   0.0019550482   0.0024289992   0.0021292434   0.0011484714 
+      3300         124   0.0016148199   0.0020062914   0.001787787    0.0010893844 
+      3400         124   0.0013434329   0.0016691136   0.0014690989   0.001325505  
+      3500         124   0.0010971454   0.00136312     0.0012496656   0.0014062237 
+      3600         124   0.00089514745  0.0011121529   0.0010349137   0.0013004041 
+      3700         124   0.00079220295  0.00098425215  0.00089325412  0.0013154029 
+      3800         124   0.00072319138  0.0008985105   0.00082122483  0.0010962257 
+      3900         124   0.00059169918  0.00073514141  0.0006832875   0.0011623171 
+      4000         124   0.00049184916  0.00061108533  0.00058188229  0.0012411181 
+      4100         124   0.00040680153  0.00050542008  0.00047870676  0.0011629016 
+      4200         124   0.00030588217  0.00038003543  0.00038246927  0.001099663  
+      4300         124   0.00026922252  0.00033448858  0.00034959953  0.0011174124 
+      4400         124   0.00022239176  0.00027630491  0.0002971948   0.0011072118 
+      4500         124   0.00020343817  0.00025275651  0.00027474732  0.0011125161 
+      4600         124   0.00020212818  0.00025112896  0.00027242474  0.0011191532 
+      4700         124   0.00018351448  0.00022800283  0.00025264863  0.0011176353 
+      4800         124   0.00018007372  0.00022372795  0.00024857425  0.0011156418 
+      4900         124   0.00015459176  0.00019206855  0.00021711531  0.0011174087 
+      5000         124   0.00013814109  0.00017162984  0.00019806357  0.0011476165 
+Loop time of 0.4577 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 4719248.480 tau/day, 10924.186 timesteps/s, 1.355 Matom-step/s
+93.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0022346  | 0.016804   | 0.033685   |  11.1 |  3.67
+Neigh   | 0.0020117  | 0.0046796  | 0.0070742  |   3.5 |  1.02
+Comm    | 0.06899    | 0.08616    | 0.10138    |   5.0 | 18.82
+Output  | 0.20305    | 0.26373    | 0.33837    |  10.2 | 57.62
+Modify  | 0.0017927  | 0.0031945  | 0.0052327  |   2.5 |  0.70
+Other   |            | 0.08314    |            |       | 18.16
+
+Nlocal:             31 ave          55 max           6 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         118 max          69 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 270
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 0 0 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         124   0.00013814109  0.00017162984  0.00019806357  0.0011393845 
+      5100         124   5.2497489      0.15227351     0.086950224    0.083018439  
+      5200         124   5.2667941      0.17345097     0.10004552     0.081933375  
+      5300         124   5.2702467      0.17774046     0.098721846    0.081858913  
+      5400         124   5.2810321      0.1911405      0.10284442     0.081908237  
+      5500         124   5.2869181      0.19845342     0.10520589     0.082475287  
+      5600         124   5.2903829      0.20275822     0.1062221      0.082060713  
+      5700         124   5.2972601      0.21130259     0.11014372     0.082904363  
+      5800         124   5.3133933      0.23134691     0.11895223     0.082638221  
+      5900         124   5.321421       0.24132073     0.12341367     0.08367512   
+      6000         124   5.3311871      0.25345436     0.1289868      0.08585114   
+      6100         124   5.3397784      0.26412833     0.13380251     0.083860885  
+      6200         124   5.3440946      0.26949097     0.13630397     0.084294896  
+      6300         124   5.3490438      0.27563994     0.13938066     0.084316514  
+      6400         124   5.3513948      0.27856086     0.14088282     0.084355453  
+      6500         124   5.3532922      0.28091822     0.14197211     0.084169662  
+      6600         124   5.3554267      0.28357014     0.14325168     0.084261645  
+      6700         124   5.3570557      0.2855941      0.14433458     0.084810743  
+      6800         124   5.360655       0.29006592     0.14636096     0.084297488  
+      6900         124   5.3655245      0.29611592     0.14908452     0.085243202  
+      7000         124   5.3671924      0.29818814     0.14990767     0.085406818  
+      7100         124   5.3695979      0.30117682     0.15113793     0.084784596  
+      7200         124   5.3704771      0.30226917     0.15173765     0.085669989  
+      7300         124   5.3706216      0.3024487      0.15180341     0.084798844  
+      7400         124   5.373135       0.30557147     0.15321903     0.085809531  
+      7500         124   5.377898       0.31148903     0.15599818     0.085242244  
+      7600         124   5.3787889      0.31259599     0.15641937     0.085326973  
+      7700         124   5.3793411      0.31328199     0.15676105     0.084950755  
+      7800         124   5.3803167      0.31449408     0.15736738     0.085202699  
+      7900         124   5.3797837      0.31383196     0.15704082     0.085404305  
+      8000         124   5.378568       0.31232146     0.15632737     0.084957387  
+      8100         124   5.3790479      0.31291774     0.15667738     0.08504012   
+      8200         124   5.3804618      0.3146744      0.15746304     0.085394022  
+      8300         124   5.381518       0.31598663     0.1580058      0.085647397  
+      8400         124   5.3814854      0.31594618     0.15794776     0.085483103  
+      8500         124   5.3828149      0.31759794     0.15875289     0.085382128  
+      8600         124   5.3832577      0.31814807     0.15901813     0.085100022  
+      8700         124   5.3838083      0.31883219     0.1593819      0.085126575  
+      8800         124   5.3842963      0.31943849     0.15972799     0.085207191  
+      8900         124   5.3846809      0.31991635     0.15992599     0.085139646  
+      9000         124   5.3850037      0.32031738     0.16014788     0.085113229  
+      9100         124   5.3849209      0.32021445     0.16009856     0.086008106  
+      9200         124   5.3851663      0.32051942     0.16025838     0.085113861  
+      9300         124   5.3847882      0.32004969     0.16001717     0.085571311  
+      9400         124   5.3845996      0.31981535     0.15990007     0.085364837  
+      9500         124   5.3847067      0.31994844     0.15998733     0.085299109  
+      9600         124   5.3849015      0.32019038     0.1601311      0.085276233  
+      9700         124   5.3850083      0.32032313     0.16021695     0.08525484   
+      9800         124   5.3852855      0.32066753     0.16041712     0.085313652  
+      9900         124   5.3850371      0.3203589      0.16026849     0.085310954  
+     10000         124   5.3851839      0.32054133     0.16038666     0.085302918  
+Loop time of 0.409799 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5270871.402 tau/day, 12201.091 timesteps/s, 1.513 Matom-step/s
+93.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0051334  | 0.025604   | 0.046384   |  12.8 |  6.25
+Neigh   | 0.0021156  | 0.0071148  | 0.012216   |   5.9 |  1.74
+Comm    | 0.074209   | 0.097182   | 0.11963    |   7.1 | 23.71
+Output  | 0.17917    | 0.21221    | 0.26696    |   7.7 | 51.78
+Modify  | 0.0025472  | 0.0042401  | 0.0062812  |   2.4 |  1.03
+Other   |            | 0.06344    |            |       | 15.48
+
+Nlocal:             31 ave          59 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:             93 ave         116 max          65 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 316
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.714 | 7.726 | 7.737 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         124   0.25799668     0.32054133     0.16038666     0.011646419  
+     10100         124   0.08324921     0.10343084     0.062335766    0.0036624752 
+     10200         124   0.055901794    0.069453744    0.049832932    0.0033728561 
+     10300         124   0.044027763    0.054701161    0.04185265     0.0026179937 
+     10400         124   0.033039084    0.04104856     0.033838053    0.0042759187 
+     10500         124   0.027910031    0.034676099    0.03032615     0.0035478069 
+     10600         124   0.023950341    0.029756484    0.027453511    0.0021787132 
+     10700         124   0.019265986    0.023936529    0.024195141    0.0021075014 
+     10800         124   0.01792324     0.022268268    0.02351488     0.0024045592 
+     10900         124   0.016637573    0.020670924    0.022003538    0.0034529435 
+     11000         124   0.01309629     0.016271149    0.019359267    0.0017153891 
+     11100         124   0.011683446    0.014515797    0.018854763    0.0026746409 
+     11200         124   0.010761235    0.013370019    0.018196576    0.0029245106 
+     11300         124   0.010091525    0.012537955    0.017818489    0.0015293592 
+     11400         124   0.0096257383   0.011959251    0.017339573    0.001738964  
+     11500         124   0.0090651598   0.011262774    0.017333091    0.001572136  
+     11600         124   0.0083289641   0.010348107    0.016333003    0.0017025439 
+     11700         124   0.0082472994   0.010246645    0.015938935    0.0014901853 
+     11800         124   0.0084807765   0.010536722    0.016623711    0.0014242448 
+     11900         124   0.007712302    0.009581951    0.016222065    0.001508232  
+     12000         124   0.0075675523   0.0094021104   0.016169534    0.0014905945 
+     12100         124   0.0079750147   0.0099083516   0.015149716    0.0018322585 
+     12200         124   0.0078458496   0.0097478738   0.015374706    0.0015492292 
+     12300         124   0.0067921053   0.0084386763   0.013486857    0.0029067448 
+     12400         124   0.0068508251   0.0085116312   0.014323963    0.0022197074 
+     12500         124   0.0066111171   0.0082138122   0.014731325    0.0019302025 
+     12600         124   0.0064707353   0.0080393984   0.014543367    0.0016587329 
+     12700         124   0.0063923274   0.0079419826   0.014294803    0.0021257946 
+     12800         124   0.0065672963   0.0081593681   0.014584204    0.0021816878 
+     12900         124   0.0059726164   0.0074205234   0.013858993    0.001530472  
+     13000         124   0.0058214195   0.0072326727   0.014246373    0.0022339129 
+     13100         124   0.0059612276   0.0074063737   0.015124804    0.0017832816 
+     13200         124   0.0054078557   0.006718851    0.014415419    0.0015478062 
+     13300         124   0.0050729677   0.0063027781   0.014411303    0.0034332889 
+     13400         124   0.0050627437   0.0062900755   0.014575044    0.0018503274 
+     13500         124   0.0046199761   0.0057399703   0.015232064    0.0015707131 
+     13600         124   0.0044802838   0.0055664132   0.015492936    0.0013436939 
+     13700         124   0.0039229012   0.0048739075   0.014834411    0.0015775897 
+     13800         124   0.0038496507   0.0047828994   0.014358939    0.0018648078 
+     13900         124   0.0038836627   0.0048251567   0.015268416    0.0016609027 
+     14000         124   0.0039681599   0.0049301381   0.015565026    0.0015819215 
+     14100         124   0.0038047814   0.0047271526   0.013834942    0.0026360599 
+     14200         124   0.0039663433   0.004927881    0.014740545    0.0017718033 
+     14300         124   0.0042501525   0.0052804925   0.015931298    0.0015106704 
+     14400         124   0.0043324422   0.0053827312   0.014699138    0.0017419936 
+     14500         124   0.0051700329   0.0064233742   0.014614744    0.0017929379 
+     14600         124   0.0051378715   0.006383416    0.015531966    0.001759876  
+     14700         124   0.0043671736   0.0054258823   0.014990071    0.0014624588 
+     14800         124   0.0045615958   0.0056674372   0.014632879    0.001980479  
+     14900         124   0.0043120591   0.0053574067   0.014648647    0.0017081314 
+     15000         124   0.0040016693   0.004971771    0.015227426    0.0014981674 
+Loop time of 0.388132 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5565117.226 tau/day, 12882.216 timesteps/s, 1.597 Matom-step/s
+90.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00066988 | 0.018356   | 0.040036   |  13.2 |  4.73
+Neigh   | 0.00064433 | 0.0021311  | 0.00401    |   3.2 |  0.55
+Comm    | 0.066969   | 0.087733   | 0.10454    |   5.6 | 22.60
+Output  | 0.1811     | 0.21514    | 0.2695     |   7.6 | 55.43
+Modify  | 0.00073098 | 0.0022522  | 0.0043484  |   3.3 |  0.58
+Other   |            | 0.06252    |            |       | 16.11
+
+Nlocal:             31 ave          54 max           8 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         116 max          70 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 88
+Dangerous builds = 0
+
+fix             1 tri move rotate 0 0 0 1 1 1 25
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.589 | 8.601 | 8.612 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         124   0.0040016693   0.004971771    0.015227426    0.0015086634 
+     15100         124   5.2391455      0.13909965     0.086544429    0.084187091  
+     15200         124   5.2856213      0.19684224     0.11745683     0.083186315  
+     15300         124   5.3131372      0.23102865     0.13493822     0.08605977   
+     15400         124   5.312441       0.23016376     0.13361748     0.085326393  
+     15500         124   5.3238039      0.24428132     0.13748765     0.083860323  
+     15600         124   5.3492159      0.27585379     0.15195482     0.090509109  
+     15700         124   5.3793259      0.31326319     0.16813451     0.094842314  
+     15800         124   5.3836817      0.31867484     0.17028976     0.089989699  
+     15900         124   5.3796952      0.31372196     0.16538847     0.094472961  
+     16000         124   5.4115814      0.3533382      0.18150785     0.091208354  
+     16100         124   5.3936511      0.33106115     0.17088137     0.093629945  
+     16200         124   5.3957378      0.33365363     0.17021817     0.099559486  
+     16300         124   5.4107263      0.35227575     0.17833256     0.097418633  
+     16400         124   5.4157911      0.35856834     0.18023194     0.094902693  
+     16500         124   5.4104949      0.35198831     0.17667749     0.098565938  
+     16600         124   5.409282       0.35048133     0.17592806     0.096041734  
+     16700         124   5.413877       0.35619023     0.1787891      0.092627526  
+     16800         124   5.41431        0.35672824     0.1791246      0.094118962  
+     16900         124   5.4131542      0.35529219     0.17881883     0.092708811  
+     17000         124   5.4141932      0.35658307     0.1798655      0.090520504  
+     17100         124   5.4220385      0.3663303      0.18519617     0.089222997  
+     17200         124   5.4046579      0.34473618     0.17738138     0.094492682  
+     17300         124   5.4056346      0.34594968     0.17932898     0.087067848  
+     17400         124   5.4625758      0.4166948      0.21590291     0.087573329  
+     17500         124   5.5101683      0.47582488     0.24840276     0.086186395  
+     17600         124   5.5878392      0.5723251      0.29850268     0.08748419   
+     17700         124   5.6772998      0.6834732      0.36153625     0.091782683  
+     17800         124   5.7649819      0.79241148     0.41944601     0.091955533  
+     17900         124   5.6293884      0.6239469      0.34262388     0.092222925  
+     18000         124   5.5993719      0.58665365     0.3202341      0.092041421  
+     18100         124   5.5929165      0.57863332     0.31757988     0.089752868  
+     18200         124   5.5194314      0.48733363     0.27391729     0.088604294  
+     18300         124   5.5558601      0.53259351     0.29860433     0.087707501  
+     18400         124   5.5243479      0.49344201     0.28138274     0.091109598  
+     18500         124   5.4712545      0.4274775      0.24899279     0.085579285  
+     18600         124   5.4614746      0.41532663     0.24277803     0.093560936  
+     18700         124   5.4335266      0.38060339     0.22486156     0.092857653  
+     18800         124   5.4062944      0.34676949     0.20805012     0.085928259  
+     18900         124   5.3680383      0.29923911     0.18445379     0.09139396   
+     19000         124   5.3612247      0.29077372     0.17705414     0.091152733  
+     19100         124   5.3657774      0.29643016     0.18163087     0.088533894  
+     19200         124   5.3753017      0.30826343     0.18731953     0.090708858  
+     19300         124   5.3788607      0.31268517     0.18511328     0.091858903  
+     19400         124   5.3753079      0.30827114     0.18028529     0.094270307  
+     19500         124   5.3793587      0.31330386     0.17822453     0.09479624   
+     19600         124   5.3794279      0.31338982     0.17247606     0.088668785  
+     19700         124   5.3883131      0.3244291      0.17733088     0.089605063  
+     19800         124   5.3862701      0.32189078     0.17600167     0.087391973  
+     19900         124   5.3627176      0.2926286      0.15793773     0.087196402  
+     20000         124   5.371666       0.30374625     0.16190487     0.08799023   
+Loop time of 0.446069 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 4842295.219 tau/day, 11209.017 timesteps/s, 1.390 Matom-step/s
+93.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.010367   | 0.024106   | 0.040606   |   8.9 |  5.40
+Neigh   | 0.004444   | 0.010596   | 0.019572   |   6.1 |  2.38
+Comm    | 0.083456   | 0.10705    | 0.1247     |   5.4 | 24.00
+Output  | 0.1825     | 0.23041    | 0.29061    |   8.5 | 51.65
+Modify  | 0.0032429  | 0.0048904  | 0.0074544  |   2.4 |  1.10
+Other   |            | 0.06902    |            |       | 15.47
+
+Nlocal:             31 ave          73 max           6 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:             93 ave         118 max          51 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 429
+Dangerous builds = 0
+
+unfix           1
+set             type 1 angmom 0.0 0.0 0.0
+Setting atom values ...
+  100 settings made for angmom
+velocity        tri set 0.0 0.0 0.0
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 7.737 | 7.746 | 7.773 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         124   0.24447869     0.30374625     0.16190487    -0.013113207  
+     20100         124   0.058472851    0.072648087    0.051241435    0.0027199931 
+     20200         124   0.052338782    0.065026972    0.04463957     0.0049181017 
+     20300         124   0.059032454    0.073343352    0.046997972    0.0036432387 
+     20400         124   0.041540522    0.051610952    0.034851914    0.0080319941 
+     20500         124   0.034253651    0.042557567    0.030035232    0.0085785376 
+     20600         124   0.027090159    0.03365747     0.025218135    0.0056701536 
+     20700         124   0.023080903    0.028676274    0.022777714    0.0021487926 
+     20800         124   0.024811993    0.030827022    0.023644112    0.0031902401 
+     20900         124   0.02296688     0.028534608    0.022697322    0.0052975401 
+     21000         124   0.024959299    0.031010038    0.023833456    0.0049399041 
+     21100         124   0.024560924    0.030515087    0.022657931    0.0034176814 
+     21200         124   0.025331395    0.031472339    0.023297144    0.0051700371 
+     21300         124   0.023119592    0.028724342    0.021901117    0.0028542595 
+     21400         124   0.021068783    0.026176367    0.02024999     0.0066313423 
+     21500         124   0.019958716    0.024797192    0.020021151    0.0054394297 
+     21600         124   0.021501915    0.026714501    0.021044833    0.003139584  
+     21700         124   0.022663473    0.028157649    0.021375039    0.0047077744 
+     21800         124   0.017783349    0.022094464    0.018460952    0.0024408478 
+     21900         124   0.017441008    0.021669131    0.017976927    0.004236632  
+     22000         124   0.016834232    0.020915258    0.017867023    0.0032297246 
+     22100         124   0.016852641    0.02093813     0.017823693    0.0031993194 
+     22200         124   0.017260002    0.021444245    0.018617101    0.001645186  
+     22300         124   0.016279285    0.020225778    0.017759307    0.0048239099 
+     22400         124   0.013098535    0.016273937    0.014976085    0.0030481479 
+     22500         124   0.01253107     0.015568906    0.014821105    0.002818037  
+     22600         124   0.013231925    0.016439664    0.014841942    0.0061556104 
+     22700         124   0.010622794    0.013198017    0.013335312    0.0032549657 
+     22800         124   0.012715053    0.01579749     0.01437656     0.0017626703 
+     22900         124   0.01207747     0.015005341    0.013708244    0.0018658438 
+     23000         124   0.010825905    0.013450367    0.01253289     0.0024262171 
+     23100         124   0.010506745    0.013053834    0.012086254    0.0013807784 
+     23200         124   0.010816779    0.013439028    0.012089622    0.0020534022 
+     23300         124   0.010541511    0.013097028    0.012162291    0.0020542813 
+     23400         124   0.0094678491   0.011763085    0.011404012    0.0011667903 
+     23500         124   0.0083682956   0.010396973    0.010273685    0.0025941956 
+     23600         124   0.0076879289   0.0095516693   0.0099437632   0.0014724848 
+     23700         124   0.0087792045   0.010907496    0.010802224    0.0017158203 
+     23800         124   0.0070944354   0.0088142985   0.010176751    0.0030678737 
+     23900         124   0.0073071217   0.0090785451   0.010067352    0.0021355515 
+     24000         124   0.007092681    0.0088121188   0.0093578983   0.0037224355 
+     24100         124   0.0061240788   0.0076087039   0.0088323652   0.00075591612
+     24200         124   0.0060997333   0.0075784566   0.0089160306   0.00074919945
+     24300         124   0.0074369071   0.0092397936   0.0098936814   0.0016742568 
+     24400         124   0.0055774041   0.0069295021   0.0089788427   0.0010941333 
+     24500         124   0.0054891817   0.0068198925   0.0089585787   0.0010201513 
+     24600         124   0.0052665503   0.0065432898   0.0085195212   0.0027803091 
+     24700         124   0.0052229505   0.0064891203   0.0083245915   0.0032441386 
+     24800         124   0.0045885549   0.0057009318   0.0077639469   0.0021437792 
+     24900         124   0.0048155198   0.0059829185   0.0082794836   0.0013531019 
+     25000         124   0.0051022231   0.0063391257   0.0084155114   0.0026277693 
+Loop time of 0.422905 on 4 procs for 5000 steps with 124 atoms
+
+Performance: 5107527.533 tau/day, 11822.980 timesteps/s, 1.466 Matom-step/s
+92.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00078007 | 0.018612   | 0.041595   |  13.3 |  4.40
+Neigh   | 0.0007419  | 0.0036728  | 0.0070159  |   4.7 |  0.87
+Comm    | 0.075945   | 0.098004   | 0.1149     |   5.5 | 23.17
+Output  | 0.17815    | 0.22946    | 0.29026    |   8.8 | 54.26
+Modify  | 0.0008285  | 0.0025442  | 0.0042422  |   3.2 |  0.60
+Other   |            | 0.07061    |            |       | 16.70
+
+Nlocal:             31 ave          58 max           5 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             93 ave         119 max          66 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 149
+Dangerous builds = 0
+
+Total wall time: 0:00:02

examples/gransurf/surf.line

@@ -0,0 +1,15 @@
+LAMMPS molecule file for line box
+
+9 lines
+
+Lines
+
+1 1 2 7 0 10 10
+2 1 2 10 10 0 7
+3 1 2 0 7 -10 10
+4 1 2 -10 10 -7 0
+5 1 2 -7 0 -10 -10
+6 1 2 -10 -10 0 -10
+7 1 2 0 -10 10 -10
+8 1 2 10 -10 10 0
+9 1 2 0 -9.9 0 -4

examples/gransurf/surf.tri

@@ -0,0 +1,10 @@
+LAMMPS data file for tri plane
+
+4 triangles
+
+Triangles
+
+1 1 2 -6 -6 0 6 -6 0 0 0 0
+2 1 2 6 -6 0 6 6 0 0 0 0
+3 1 2 6 6 0 -6 6 0 0 0 0
+4 1 2 -6 -6 0 0 0 0 -6 6 0

examples/gransurf/surf.tri.stl

@@ -0,0 +1,30 @@
+solid STL version of surf.tri
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6 -6 0
+      vertex 6 -6 0
+      vertex 0 0 0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6 -6 0
+      vertex 6 6 0
+      vertex 0 0 0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6 6 0
+      vertex -6 6 0
+      vertex 0 0 0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6 -6 0
+      vertex 0 0 0
+      vertex -6 6 0
+    endloop
+  endfacet
+endsolid STL version of surf.tri

examples/gransurf/surf.tribox

@@ -0,0 +1,31 @@
+LAMMPS data file for tri box
+
+24 triangles
+
+Triangles
+
+1 1 2   0.0 0.0 -6.0 6.0 6.0 -6.0 6.0 -6.0 -6.0
+2 1 2   0.0 0.0 6.0 6.0 -6.0 6.0 6.0 6.0 6.0
+3 1 2   0.0 0.0 6.0 -6.0 -6.0 6.0 6.0 -6.0 6.0
+4 1 2   -6.0 6.0 6.0 -6.0 -6.0 6.0 0.0 0.0 6.0
+5 1 2   -6.0 -6.0 -6.0 0.0 0.0 -6.0 6.0 -6.0 -6.0
+6 1 2   0.0 0.0 -6.0 -6.0 -6.0 -6.0 -6.0 6.0 -6.0
+7 1 2   0.0 0.0 6.0 6.0 6.0 6.0 -6.0 6.0 6.0
+8 1 2   6.0 6.0 -6.0 0.0 0.0 -6.0 -6.0 6.0 -6.0
+9 1 2   6.0 6.0 -6.0 0.0 6.0 0.0 6.0 6.0 6.0
+10 1 2  0.0 6.0 0.0 -6.0 6.0 6.0 6.0 6.0 6.0
+11 1 2  6.0 -6.0 6.0 0.0 -6.0 0.0 6.0 -6.0 -6.0
+12 1 2  0.0 -6.0 0.0 6.0 -6.0 6.0 -6.0 -6.0 6.0
+13 1 2  0.0 6.0 0.0 6.0 6.0 -6.0 -6.0 6.0 -6.0
+14 1 2  -6.0 6.0 6.0 0.0 6.0 0.0 -6.0 6.0 -6.0
+15 1 2  0.0 -6.0 0.0 -6.0 -6.0 -6.0 6.0 -6.0 -6.0
+16 1 2  0.0 -6.0 0.0 -6.0 -6.0 6.0 -6.0 -6.0 -6.0
+17 1 2  6.0 6.0 6.0 6.0 0.0 0.0 6.0 6.0 -6.0
+18 1 2  6.0 0.0 0.0 6.0 -6.0 -6.0 6.0 6.0 -6.0
+19 1 2  -6.0 6.0 -6.0 -6.0 0.0 0.0 -6.0 6.0 6.0
+20 1 2  -6.0 0.0 0.0 -6.0 6.0 -6.0 -6.0 -6.0 -6.0
+21 1 2  6.0 0.0 0.0 6.0 6.0 6.0 6.0 -6.0 6.0
+22 1 2  6.0 -6.0 -6.0 6.0 0.0 0.0 6.0 -6.0 6.0
+23 1 2  -6.0 0.0 0.0 -6.0 -6.0 6.0 -6.0 6.0 6.0
+24 1 2  -6.0 0.0 0.0 -6.0 -6.0 -6.0 -6.0 -6.0 6.0
+ 

examples/gransurf/surf.tribox.stl

@@ -0,0 +1,171 @@
+solid STL version of surf.tribox
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 0.0 -6.0
+      vertex 6.0 6.0 -6.0
+      vertex 6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 0.0 6.0
+      vertex 6.0 -6.0 6.0
+      vertex 6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 0.0 6.0
+      vertex -6.0 -6.0 6.0
+      vertex 6.0 -6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 6.0 6.0
+      vertex -6.0 -6.0 6.0
+      vertex 0.0 0.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 -6.0 -6.0
+      vertex 0.0 0.0 -6.0
+      vertex 6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 0.0 -6.0
+      vertex -6.0 -6.0 -6.0
+      vertex -6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 0.0 6.0
+      vertex 6.0 6.0 6.0
+      vertex -6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 6.0 -6.0
+      vertex 0.0 0.0 -6.0
+      vertex -6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 6.0 -6.0
+      vertex 0.0 6.0 0.0
+      vertex 6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 6.0 0.0
+      vertex -6.0 6.0 6.0
+      vertex 6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 -6.0 6.0
+      vertex 0.0 -6.0 0.0
+      vertex 6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 -6.0 0.0
+      vertex 6.0 -6.0 6.0
+      vertex -6.0 -6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 6.0 0.0
+      vertex 6.0 6.0 -6.0
+      vertex -6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 6.0 6.0
+      vertex 0.0 6.0 0.0
+      vertex -6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 -6.0 0.0
+      vertex -6.0 -6.0 -6.0
+      vertex 6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 0.0 -6.0 0.0
+      vertex -6.0 -6.0 6.0
+      vertex -6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 6.0 6.0
+      vertex 6.0 0.0 0.0
+      vertex 6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 0.0 0.0
+      vertex 6.0 -6.0 -6.0
+      vertex 6.0 6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 6.0 -6.0
+      vertex -6.0 0.0 0.0
+      vertex -6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 0.0 0.0
+      vertex -6.0 6.0 -6.0
+      vertex -6.0 -6.0 -6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 0.0 0.0
+      vertex 6.0 6.0 6.0
+      vertex 6.0 -6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex 6.0 -6.0 -6.0
+      vertex 6.0 0.0 0.0
+      vertex 6.0 -6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 0.0 0.0
+      vertex -6.0 -6.0 6.0
+      vertex -6.0 6.0 6.0
+    endloop
+  endfacet
+  facet normal 0.0 0.0 0.0
+    outer loop
+      vertex -6.0 0.0 0.0
+      vertex -6.0 -6.0 -6.0
+      vertex -6.0 -6.0 6.0
+    endloop
+  endfacet
+endsolid STL version of surf.tribox
+

src/.gitignore

@@ -1045,6 +1045,12 @@
 /fix_srd.h
 /fix_store_kim.cpp
 /fix_store_kim.h
+/fix_surface.cpp
+/fix_surface.h
+/fix_surface_global.cpp
+/fix_surface_global.h
+/fix_surface_local.cpp
+/fix_surface_local.h
 /fix_temp_rescale_eff.cpp
 /fix_temp_rescale_eff.h
 /fix_tgnh_drude.cpp
@@ -1269,6 +1275,8 @@
 /pair_gran_hooke.h
 /pair_gran_hooke_history.cpp
 /pair_gran_hooke_history.h
+/pair_surf_granular.cpp
+/pair_surf_granular.h
 /pair_gw.cpp
 /pair_gw.h
 /pair_gw_zbl.cpp
@@ -1297,6 +1305,10 @@
 /pair_lebedeva_z.h
 /pair_line_lj.cpp
 /pair_line_lj.h
+/pair_line_gran_hooke.cpp
+/pair_line_gran_hooke.h
+/pair_line_gran_hooke_history.cpp
+/pair_line_gran_hooke_history.h
 /pair_list.cpp
 /pair_list.h
 /pair_lj_charmm_coul_charmm.cpp
@@ -1472,6 +1484,10 @@
 /pair_tracker.cpp
 /pair_tri_lj.cpp
 /pair_tri_lj.h
+/pair_tri_gran_hooke.cpp
+/pair_tri_gran_hooke.h
+/pair_tri_gran_hooke_history.cpp
+/pair_tri_gran_hooke_history.h
 /pair_yukawa_colloid.cpp
 /pair_yukawa_colloid.h
 /pair_wf_cut.cpp
@@ -1558,6 +1574,8 @@
 /smd_material_models.cpp
 /smd_material_models.h
 /smd_math.h
+/surf_extra.cpp
+/surf_extra.h
 /tad.cpp
 /tad.h
 /temper.cpp

src/GRANSURF/fix_surface.cpp

@@ -0,0 +1,672 @@
+/* ----------------------------------------------------------------------
+   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_surface.h"
+
+#include "atom.h"
+#include "domain.h"
+#include "error.h"
+#include "memory.h"
+#include "molecule.h"
+#include "stl_reader.h"
+
+using namespace LAMMPS_NS;
+
+static constexpr int DELTA = 128;
+
+/* ---------------------------------------------------------------------- */
+
+FixSurface::FixSurface(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) {}
+
+/* ---------------------------------------------------------------------- */
+
+FixSurface::~FixSurface() {}
+
+/* ----------------------------------------------------------------------
+   extract lines or tris from a molecule template ID for one or more molecules
+   concatenate into single list of points and lines or tris
+   identify unique points using hash
+------------------------------------------------------------------------- */
+
+void FixSurface::extract_from_molecule(char *molID,
+                                       std::map<std::tuple<double,double,double>,int> *hash,
+                                       int &npoints, int &maxpoints,
+                                       Point *&points, int &nlines, Line *&lines,
+                                       int &ntris, Tri *&tris)
+{
+  int dimension = domain->dimension;
+
+  int imol = atom->find_molecule(molID);
+  if (imol == -1)
+    error->all(FLERR,"Molecule template ID for fix surface does not exist");
+
+  // loop over one or more molecules in molID
+
+  Molecule **onemols = &atom->molecules[imol];
+  int nmol = onemols[0]->nset;
+
+  for (int m = 0; m < nmol; m++) {
+    if (dimension == 2)
+      if (onemols[m]->lineflag == 0)
+        error->all(FLERR,"Fix surface molecule must have lines");
+    if (dimension == 3)
+      if (onemols[m]->triflag == 0)
+        error->all(FLERR,"Fix surface molecule must have triangles");
+
+    int nl = onemols[m]->nlines;
+    int nt = onemols[m]->ntris;
+
+    nlines += nl;
+    ntris += nt;
+    lines = (Line *) memory->srealloc(lines,nlines*sizeof(Line),
+                                      "surface:lines");
+    tris = (Tri *) memory->srealloc(tris,ntris*sizeof(Tri),
+                                    "surface:tris");
+
+    // offset line/tri index lists by previous npoints
+    // pi,p2,p3 are C-style indices into points vector
+
+    if (dimension == 2) {
+      int *molline = onemols[m]->molline;
+      int *typeline = onemols[m]->typeline;
+      double **epts = onemols[m]->lines;
+      int iline = nlines - nl;
+
+      for (int i = 0; i < nl; i++) {
+        lines[iline].mol = molline[i];
+        lines[iline].type = typeline[i];
+
+        auto key = std::make_tuple(epts[i][0],epts[i][1],0.0);
+        if (hash->find(key) == hash->end()) {
+          if (npoints == maxpoints) {
+            maxpoints += DELTA;
+            points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                                "surface:points");
+          }
+          (*hash)[key] = npoints;
+          points[npoints].x[0] = epts[i][0];
+          points[npoints].x[1] = epts[i][1];
+          points[npoints].x[2] = 0.0;
+          lines[iline].p1 = npoints;
+          npoints++;
+        } else lines[iline].p1 = (*hash)[key];
+
+        key = std::make_tuple(epts[i][2],epts[i][3],0.0);
+        if (hash->find(key) == hash->end()) {
+          if (npoints == maxpoints) {
+            maxpoints += DELTA;
+            points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                                "surface:points");
+          }
+          (*hash)[key] = npoints;
+          points[npoints].x[0] = epts[i][2];
+          points[npoints].x[1] = epts[i][3];
+          points[npoints].x[2] = 0.0;
+          lines[iline].p2 = npoints;
+          npoints++;
+        } else lines[iline].p2 = (*hash)[key];
+
+        iline++;
+      }
+    }
+
+    if (dimension == 3) {
+      int *moltri = onemols[m]->moltri;
+      int *typetri = onemols[m]->typetri;
+      double **cpts = onemols[m]->tris;
+      int itri = ntris - nt;
+
+      for (int i = 0; i < nt; i++) {
+        tris[itri].mol = moltri[i];
+        tris[itri].type = typetri[i];
+
+        auto key = std::make_tuple(cpts[i][0],cpts[i][1],cpts[i][2]);
+        if (hash->find(key) == hash->end()) {
+          if (npoints == maxpoints) {
+            maxpoints += DELTA;
+            points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                                "surface:points");
+          }
+          (*hash)[key] = npoints;
+          points[npoints].x[0] = cpts[i][0];
+          points[npoints].x[1] = cpts[i][1];
+          points[npoints].x[2] = cpts[i][2];
+          tris[itri].p1 = npoints;
+          npoints++;
+        } else tris[itri].p1 = (*hash)[key];
+
+        key = std::make_tuple(cpts[i][3],cpts[i][4],cpts[i][5]);
+        if (hash->find(key) == hash->end()) {
+          if (npoints == maxpoints) {
+            maxpoints += DELTA;
+            points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                                "surface:points");
+          }
+          (*hash)[key] = npoints;
+          points[npoints].x[0] = cpts[i][3];
+          points[npoints].x[1] = cpts[i][4];
+          points[npoints].x[2] = cpts[i][5];
+          tris[itri].p2 = npoints;
+          npoints++;
+        } else tris[itri].p2 = (*hash)[key];
+
+        key = std::make_tuple(cpts[i][6],cpts[i][7],cpts[i][8]);
+        if (hash->find(key) == hash->end()) {
+          if (npoints == maxpoints) {
+            maxpoints += DELTA;
+            points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                                "surface:points");
+          }
+          (*hash)[key] = npoints;
+          points[npoints].x[0] = cpts[i][6];
+          points[npoints].x[1] = cpts[i][7];
+          points[npoints].x[2] = cpts[i][8];
+          tris[itri].p3 = npoints;
+          npoints++;
+        } else tris[itri].p3 = (*hash)[key];
+
+        itri++;
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   extract triangles from an STL file, can be text or binary
+   concatenate into single list of points and tris
+   identify unique points using hash
+------------------------------------------------------------------------- */
+
+void FixSurface::extract_from_stlfile(char *filename, int stype,
+                                      std::map<std::tuple<double,double,double>,int> *hash,
+                                      int &npoints, int &maxpoints,
+                                      Point *&points, int &ntris, Tri *&tris)
+{
+  if (domain->dimension == 2)
+    error->all(FLERR,"Fix surface cannot use an STL file for 2d simulations");
+
+  // read tris from STL file
+  // stltris = tri coords internal to STL reader
+
+  STLReader *stl = new STLReader(lmp);
+  double **stltris;
+  ntris = stl->read_file(filename,stltris);
+
+  tris = (Tri *) memory->srealloc(tris,ntris*sizeof(Tri),"surface:tris");
+
+  // loop over STL tris
+  // populate points and tris data structs
+  // for each tri: set molID = 1 and type = stype
+
+  for (int itri = 0; itri < ntris; itri++) {
+    tris[itri].mol = 1;
+    tris[itri].type = stype;
+
+    auto key = std::make_tuple(stltris[itri][0],stltris[itri][1],stltris[itri][2]);
+    if (hash->find(key) == hash->end()) {
+      if (npoints == maxpoints) {
+        maxpoints += DELTA;
+        points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                            "surface:points");
+      }
+      (*hash)[key] = npoints;
+      points[npoints].x[0] = stltris[itri][0];
+      points[npoints].x[1] = stltris[itri][1];
+      points[npoints].x[2] = stltris[itri][2];
+      tris[itri].p1 = npoints;
+      npoints++;
+    } else tris[itri].p1 = (*hash)[key];
+
+    key = std::make_tuple(stltris[itri][3],stltris[itri][4],stltris[itri][5]);
+    if (hash->find(key) == hash->end()) {
+      if (npoints == maxpoints) {
+        maxpoints += DELTA;
+        points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                            "surface:points");
+      }
+      (*hash)[key] = npoints;
+      points[npoints].x[0] = stltris[itri][3];
+      points[npoints].x[1] = stltris[itri][4];
+      points[npoints].x[2] = stltris[itri][5];
+      tris[itri].p2 = npoints;
+      npoints++;
+    } else tris[itri].p2 = (*hash)[key];
+
+    key = std::make_tuple(stltris[itri][6],stltris[itri][7],stltris[itri][8]);
+    if (hash->find(key) == hash->end()) {
+      if (npoints == maxpoints) {
+        maxpoints += DELTA;
+        points = (Point *) memory->srealloc(points,maxpoints*sizeof(Point),
+                                            "surface:points");
+      }
+      (*hash)[key] = npoints;
+      points[npoints].x[0] = stltris[itri][6];
+      points[npoints].x[1] = stltris[itri][7];
+      points[npoints].x[2] = stltris[itri][8];
+      tris[itri].p3 = npoints;
+      npoints++;
+    } else tris[itri].p3 = (*hash)[key];
+  }
+
+  // delete STL reader
+
+  delete stl;
+}
+
+/* ----------------------------------------------------------------------
+   create and initialize Connect2d info for global lines
+   global lines were read from molecule file(s)
+   creates connect2d data structs
+------------------------------------------------------------------------- */
+
+void FixSurface::connectivity2d_global(int npoints, int nlines, Line *lines,
+                                       Connect2d *&connect2d,
+                                       int **&neigh_p1, int **&neigh_p2)
+{
+  connect2d = (Connect2d *)
+    memory->smalloc(nlines*sizeof(Connect2d),"surface:connect2d");
+
+  // setup line end point connectivity lists
+  // counts = # of lines containing each end point (including self)
+  // plines = ragged 2d array with indices of lines which contain each point
+
+  int *counts;
+  memory->create(counts,npoints,"surface:counts");
+
+  for (int i = 0; i < npoints; i++) counts[i] = 0;
+
+  for (int i = 0; i < nlines; i++) {
+    counts[lines[i].p1]++;
+    counts[lines[i].p2]++;
+  }
+
+  int **plines;
+  memory->create_ragged(plines,npoints,counts,"surface:plines");
+
+  for (int i = 0; i < npoints; i++) counts[i] = 0;
+
+  for (int i = 0; i < nlines; i++) {
+    plines[lines[i].p1][counts[lines[i].p1]++] = i;
+    plines[lines[i].p2][counts[lines[i].p2]++] = i;
+  }
+
+  // p12_counts = # of lines connecting to endpoints p12 of each line
+  // do NOT include self
+
+  int *p1_counts,*p2_counts;
+  memory->create(p1_counts,nlines,"surface:p1_counts");
+  memory->create(p2_counts,nlines,"surface:p2_counts");
+
+  for (int i = 0; i < nlines; i++) {
+    p1_counts[i] = counts[lines[i].p1] - 1;
+    p2_counts[i] = counts[lines[i].p2] - 1;
+  }
+
+  // allocate all ragged arrays which Connect2d will point to
+
+  memory->create_ragged(neigh_p1,nlines,p1_counts,"surface:neigh_p1");
+  memory->create_ragged(neigh_p2,nlines,p2_counts,"surface:neigh_p2");
+
+  // set connect2d vector ptrs to rows of corresponding ragged arrays
+
+  for (int i = 0; i < nlines; i++) {
+    connect2d[i].np1 = p1_counts[i];
+    if (connect2d[i].np1 == 0) connect2d[i].neigh_p1 = nullptr;
+    else connect2d[i].neigh_p1 = neigh_p1[i];
+
+    connect2d[i].np2 = p2_counts[i];
+    if (connect2d[i].np2 == 0) connect2d[i].neigh_p2 = nullptr;
+    else connect2d[i].neigh_p2 = neigh_p2[i];
+  }
+
+  // initialize connect2d neigh vectors for each end point of each line
+  // do NOT include self
+
+  int j,m;
+
+  for (int i = 0; i < nlines; i++) {
+    if (p1_counts[i]) {
+      j = 0;
+      for (m = 0; m <= p1_counts[i]; m++) {
+        if (plines[lines[i].p1][m] == i) continue;
+        connect2d[i].neigh_p1[j] = plines[lines[i].p1][m];
+        j++;
+      }
+    }
+    if (p2_counts[i]) {
+      j = 0;
+      for (m = 0; m <= p2_counts[i]; m++) {
+        if (plines[lines[i].p2][m] == i) continue;
+        connect2d[i].neigh_p2[j] = plines[lines[i].p2][m];
+        j++;
+      }
+    }
+  }
+
+  // deallocate counts, plines, p12_counts
+
+  memory->destroy(counts);
+  memory->destroy(plines);
+  memory->destroy(p1_counts);
+  memory->destroy(p2_counts);
+}
+
+/* ----------------------------------------------------------------------
+   create and initialize Connect3d info for global triangles
+   global triangles were read from molecule or STL file(s)
+   creates connect3d data structs
+------------------------------------------------------------------------- */
+
+int FixSurface::connectivity3d_global(int npoints, int ntris, Tri *tris,
+                                      Connect3d *&connect3d,
+                                      int **&neigh_e1, int **&neigh_e2,
+                                      int **&neigh_e3,
+                                      int **&neigh_c1, int **&neigh_c2,
+                                      int **&neigh_c3)
+{
+  int p1,p2,p3;
+
+  connect3d = (Connect3d *)
+    memory->smalloc(ntris*sizeof(Connect3d),"surface:connect3d");
+
+  // create hash = map of unique edges
+  //   key = <p1,p2> indices of 2 points, in either order
+  //   value = index of the unique edge (0 to Nedge-1)
+  // tri2edges[i][j] = index of unique edge for tri I and edge J
+  // nedges = total count of unique edges, returned
+
+  int **tri2edge;
+  memory->create(tri2edge,ntris,3,"surface::tri2edge");
+
+  std::map<std::tuple<int,int>,int> hash;
+  int nedges = 0;
+
+  for (int i = 0; i < ntris; i++) {
+    p1 = tris[i].p1;
+    p2 = tris[i].p2;
+    p3 = tris[i].p3;
+
+    auto key1 = std::make_tuple(p1,p2);
+    auto key2 = std::make_tuple(p2,p1);
+
+    if (hash.find(key1) == hash.end() && hash.find(key2) == hash.end()) {
+      hash[key1] = nedges;
+      tri2edge[i][0] = nedges;
+      nedges++;
+    }
+    else if (hash.find(key1) != hash.end()) tri2edge[i][0] = hash[key1];
+    else if (hash.find(key2) != hash.end()) tri2edge[i][0] = hash[key2];
+
+    key1 = std::make_tuple(p2,p3);
+    key2 = std::make_tuple(p3,p2);
+
+    if (hash.find(key1) == hash.end() && hash.find(key2) == hash.end()) {
+      hash[key1] = nedges;
+      tri2edge[i][1] = nedges;
+      nedges++;
+    }
+    else if (hash.find(key1) != hash.end()) tri2edge[i][1] = hash[key1];
+    else if (hash.find(key2) != hash.end()) tri2edge[i][1] = hash[key2];
+
+    key1 = std::make_tuple(p3,p1);
+    key2 = std::make_tuple(p1,p3);
+
+    if (hash.find(key1) == hash.end() && hash.find(key2) == hash.end()) {
+      hash[key1] = nedges;
+      tri2edge[i][2] = nedges;
+      nedges++;
+    }
+    else if (hash.find(key1) != hash.end()) tri2edge[i][2] = hash[key1];
+    else if (hash.find(key2) != hash.end()) tri2edge[i][2] = hash[key2];
+  }
+
+  // setup tri edge connectivity lists
+  // counts = # of tris containing each edge (including self)
+  // etris = ragged 2d array with indices of tris which contain each edge
+
+  int *counts;
+  memory->create(counts,nedges,"surface:count");
+
+  for (int i = 0; i < nedges; i++) counts[i] = 0;
+
+  for (int i = 0; i < ntris; i++) {
+    counts[tri2edge[i][0]]++;
+    counts[tri2edge[i][1]]++;
+    counts[tri2edge[i][2]]++;
+  }
+
+  int **etris;
+  memory->create_ragged(etris,nedges,counts,"surface:etris");
+
+  for (int i = 0; i < nedges; i++) counts[i] = 0;
+
+  for (int i = 0; i < ntris; i++) {
+    etris[tri2edge[i][0]][counts[tri2edge[i][0]]++] = i;
+    etris[tri2edge[i][1]][counts[tri2edge[i][1]]++] = i;
+    etris[tri2edge[i][2]][counts[tri2edge[i][2]]++] = i;
+  }
+
+  // e123_counts = # of edges connecting to edges e123 of each tri
+  // do NOT include self
+
+  int *e1_counts,*e2_counts,*e3_counts;
+  memory->create(e1_counts,ntris,"surface:e1_counts");
+  memory->create(e2_counts,ntris,"surface:e2_counts");
+  memory->create(e3_counts,ntris,"surface:e3_counts");
+
+  for (int i = 0; i < ntris; i++) {
+    e1_counts[i] = counts[tri2edge[i][0]] - 1;
+    e2_counts[i] = counts[tri2edge[i][1]] - 1;
+    e3_counts[i] = counts[tri2edge[i][2]] - 1;
+  }
+
+  // allocate all edge ragged arrays which Connect3d will point to
+
+  memory->create_ragged(neigh_e1,ntris,e1_counts,"surface:neigh_e1");
+  memory->create_ragged(neigh_e2,ntris,e2_counts,"surface:neigh_e2");
+  memory->create_ragged(neigh_e3,ntris,e3_counts,"surface:neigh_e3");
+
+  // set connect3d edge vector ptrs to rows of corresponding edge ragged arrays
+
+  for (int i = 0; i < ntris; i++) {
+    connect3d[i].ne1 = e1_counts[i];
+    if (connect3d[i].ne1 == 0) connect3d[i].neigh_e1 = nullptr;
+    else connect3d[i].neigh_e1 = neigh_e1[i];
+
+    connect3d[i].ne2 = e2_counts[i];
+    if (connect3d[i].ne2 == 0) connect3d[i].neigh_e2 = nullptr;
+    else connect3d[i].neigh_e2 = neigh_e2[i];
+
+    connect3d[i].ne3 = e3_counts[i];
+    if (connect3d[i].ne3 == 0) connect3d[i].neigh_e3 = nullptr;
+    else connect3d[i].neigh_e3 = neigh_e3[i];
+  }
+
+  // initialize connect3d edge neigh vectors for each edge of each tri
+  // do NOT include self
+
+  int j,m;
+
+  for (int i = 0; i < ntris; i++) {
+    if (connect3d[i].ne1) {
+      j = 0;
+      for (m = 0; m < counts[tri2edge[i][0]]; m++) {
+        if (etris[tri2edge[i][0]][m] == i) continue;
+        connect3d[i].neigh_e1[j] = etris[tri2edge[i][0]][m];
+        j++;
+      }
+    }
+    if (connect3d[i].ne2) {
+      j = 0;
+      for (m = 0; m < counts[tri2edge[i][1]]; m++) {
+        if (etris[tri2edge[i][1]][m] == i) continue;
+        connect3d[i].neigh_e2[j] = etris[tri2edge[i][1]][m];
+        j++;
+      }
+    }
+    if (connect3d[i].ne3) {
+      j = 0;
+      for (m = 0; m < counts[tri2edge[i][2]]; m++) {
+        if (etris[tri2edge[i][2]][m] == i) continue;
+        connect3d[i].neigh_e3[j] = etris[tri2edge[i][2]][m];
+        j++;
+      }
+    }
+  }
+
+  // deallocate counts, tri2edge, etris, e123_counts
+
+  memory->destroy(counts);
+  memory->destroy(tri2edge);
+  memory->destroy(etris);
+  memory->destroy(e1_counts);
+  memory->destroy(e2_counts);
+  memory->destroy(e3_counts);
+
+  // setup tri corner point connectivity lists
+  // counts = # of tris containing each corner point (including self)
+  // ctris = ragged 2d array with indices of tris which contain each point
+
+  memory->create(counts,npoints,"surface:counts");
+
+  for (int i = 0; i < npoints; i++) counts[i] = 0;
+
+  for (int i = 0; i < ntris; i++) {
+    counts[tris[i].p1]++;
+    counts[tris[i].p2]++;
+    counts[tris[i].p3]++;
+  }
+
+  int **ctris;
+  memory->create_ragged(ctris,npoints,counts,"surface:ctris");
+
+  for (int i = 0; i < npoints; i++) counts[i] = 0;
+
+  for (int i = 0; i < ntris; i++) {
+    ctris[tris[i].p1][counts[tris[i].p1]++] = i;
+    ctris[tris[i].p2][counts[tris[i].p2]++] = i;
+    ctris[tris[i].p3][counts[tris[i].p3]++] = i;
+  }
+
+  // c123_counts = # of tris connecting to corner points c123 of each tri
+  // do NOT include self or tris which connect to an edge
+  // only include tris which only connect at the corner point
+
+  int *c1_counts,*c2_counts,*c3_counts;
+  memory->create(c1_counts,ntris,"surface:c1_counts");
+  memory->create(c2_counts,ntris,"surface:c2_counts");
+  memory->create(c3_counts,ntris,"surface:c3_counts");
+
+  for (int i = 0; i < ntris; i++) {
+    c1_counts[i] = counts[tris[i].p1] - 1;
+    c1_counts[i] -= connect3d[i].ne3 + connect3d[i].ne1;
+    c2_counts[i] = counts[tris[i].p2] - 1;
+    c2_counts[i] -= connect3d[i].ne1 + connect3d[i].ne2;
+    c3_counts[i] = counts[tris[i].p3] - 1;
+    c3_counts[i] -= connect3d[i].ne2 + connect3d[i].ne3;
+  }
+
+  // allocate all corner ragged arrays which Connect3d will point to
+
+  memory->create_ragged(neigh_c1,ntris,c1_counts,"surface:neigh_c1");
+  memory->create_ragged(neigh_c2,ntris,c2_counts,"surface:neigh_c2");
+  memory->create_ragged(neigh_c3,ntris,c3_counts,"surface:neigh_c3");
+
+  // set connect3d corner vector ptrs to rows of corresponding corner ragged arrays
+
+  for (int i = 0; i < ntris; i++) {
+    connect3d[i].nc1 = c1_counts[i];
+    if (connect3d[i].nc1) connect3d[i].neigh_c1 = neigh_c1[i];
+    else connect3d[i].neigh_c1 = nullptr;
+
+    connect3d[i].nc2 = c2_counts[i];
+    if (connect3d[i].nc2) connect3d[i].neigh_c2 = neigh_c2[i];
+    else connect3d[i].neigh_c2 = nullptr;
+
+    connect3d[i].nc3 = c3_counts[i];
+    if (connect3d[i].nc3) connect3d[i].neigh_c3 = neigh_c3[i];
+    else connect3d[i].neigh_c3 = nullptr;
+  }
+
+  // initialize connect3d corner neigh vectors for each corner of each tri
+  // do NOT include self or tris which connect to an edge
+  // only include tris which only connect at the corner point
+
+  int n,medge,skipflag;
+
+  for (int i = 0; i < ntris; i++) {
+    if (connect3d[i].nc1) {
+      j = 0;
+      for (m = 0; m < counts[tris[i].p1]; m++) {
+        n = ctris[tris[i].p1][m];
+        if (n == i) continue;
+
+        skipflag = 0;
+        for (medge = 0; medge < connect3d[i].ne3; medge++)
+          if (n == connect3d[i].neigh_e3[medge]) skipflag = 1;
+        for (medge = 0; medge < connect3d[i].ne1; medge++)
+          if (n == connect3d[i].neigh_e1[medge]) skipflag = 1;
+        if (skipflag) continue;
+
+        connect3d[i].neigh_c1[j] = n;
+        j++;
+      }
+    }
+    if (connect3d[i].nc2) {
+      j = 0;
+      for (m = 0; m < counts[tris[i].p2]; m++) {
+        n = ctris[tris[i].p2][m];
+        if (n == i) continue;
+
+        skipflag = 0;
+        for (medge = 0; medge < connect3d[i].ne1; medge++)
+          if (n == connect3d[i].neigh_e1[medge]) skipflag = 1;
+        for (medge = 0; medge < connect3d[i].ne2; medge++)
+          if (n == connect3d[i].neigh_e2[medge]) skipflag = 1;
+        if (skipflag) continue;
+
+        connect3d[i].neigh_c2[j] = n;
+        j++;
+      }
+    }
+    if (connect3d[i].nc3) {
+      j = 0;
+      for (m = 0; m < counts[tris[i].p3]; m++) {
+        n = ctris[tris[i].p3][m];
+        if (n == i) continue;
+
+        skipflag = 0;
+        for (medge = 0; medge < connect3d[i].ne2; medge++)
+          if (n == connect3d[i].neigh_e2[medge]) skipflag = 1;
+        for (medge = 0; medge < connect3d[i].ne3; medge++)
+          if (n == connect3d[i].neigh_e3[medge]) skipflag = 1;
+        if (skipflag) continue;
+
+        connect3d[i].neigh_c3[j] = n;
+        j++;
+      }
+    }
+  }
+
+  // deallocate counts, ctris, c123_counts
+
+  memory->destroy(counts);
+  memory->destroy(ctris);
+  memory->destroy(c1_counts);
+  memory->destroy(c2_counts);
+  memory->destroy(c3_counts);
+
+  // return edge count
+
+  return nedges;
+}

src/GRANSURF/fix_surface.h

@@ -0,0 +1,145 @@
+/* -*- 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_FIX_SURFACE_H
+#define LMP_FIX_SURFACE_H
+
+#include "fix.h"
+#include <map>
+#include <tuple>
+
+namespace LAMMPS_NS {
+
+class FixSurface : public Fix {
+ public:
+
+  // connectivity info between lines or tris
+
+  struct Connect2d {      // line connectivity
+
+                          // counts, not including self
+    int np1,np2;          // # of lines connected to endpts 1/2
+
+    int exposed_pt[2];    // whether p1 and p2 are exposed
+
+                          // pairs of endpoint connections
+    tagint *neigh_p1;     // indices (or IDs) of lines connected to endpt 1
+    tagint *neigh_p2;     // ditto for connections to endpt 2
+    int *pwhich_p1;       // which point (0,1) on other line is endpt 1
+    int *pwhich_p2;       // ditto for endpt 2
+    int *nside_p1;        // consistency of other line normal
+    int *nside_p2;        // ditto for endpt 2
+                          //   SAME_SIDE = 2 normals are on same side of surf
+                          //   OPPOSITE_SIDE = opposite sides of surf
+    int *aflag_p1;        // is this line + other line a FLAT,CONCAVE,CONVEX surf
+    int *aflag_p2;        // ditto for endpt 2
+                          //   surf = on normal side of this line
+                          //   aflag = FLAT, CONCAVE, CONVEX
+  };
+
+  struct Connect3d {      // tri connectivity
+
+                          // counts, not including self
+                          // also not including edge-connected tris for corner pts
+    int ne1,ne2,ne3;      // # of tris connected to edges 1,2,3
+    int nc1,nc2,nc3;      // # of tris connected to corner pts 1,2,3
+
+    int exposed_pt[3];    // whether p1, p2, and p3 are exposed
+    int exposed_edge[3];  // whether e1, e2, and e3 are exposed
+
+                          // pairs of edge connections
+    tagint *neigh_e1;     // indices (or IDs) of tris connected to edge 1
+    tagint *neigh_e2;     // ditto for connections to edge 2
+    tagint *neigh_e3;     // ditto for connections to edge 3
+    int *ewhich_e1;       // which edge (0,1,2) on other tri shares edge 1
+    int *ewhich_e2;       // ditto for edge 2
+    int *ewhich_e3;       // ditto for edge 3
+    int *nside_e1;        // consistency of other tri normal
+    int *nside_e2;        // ditto for edge 2
+    int *nside_e3;        // ditto for edge 3
+                          //   SAME_SIDE = 2 normals are on same side of surf
+                          //   OPPOSITE_SIDE = opposite sides of surf
+    int *aflag_e1;        // is this tri + other tri a FLAT,CONCAVE,CONVEX surf
+    int *aflag_e2;        // ditto for edge 2
+    int *aflag_e3;        // ditto for edge 3
+                          //   surf = on normal side of this tri
+                          //   aflag = FLAT, CONCAVE, CONVEX
+
+                          // pairs of corner pt connections
+    tagint *neigh_c1;     // indices (or IDs) of tris connected to corner pt 1
+    tagint *neigh_c2;     // ditto for connections to corner pt 2
+    tagint *neigh_c3;     // ditto for connections to corner pt 3
+    int *cwhich_c1;       // which corner pt (0,1,2) on other tri shares corner pt 1
+    int *cwhich_c2;       // ditto for corner pt 2
+    int *cwhich_c3;       // ditto for corner pt 3
+    int *nside_c1;        // consistency of normals, only meaningful for FLAT
+    int *nside_c2;        // ditto for corner 2
+    int *nside_c3;        // ditto for corner 3
+    int *aflag_c1;        // are tris FLAT or CONCAVE (no CONVEX)
+    int *aflag_c2;        // ditto for corner 2
+    int *aflag_c3;        // ditto for corner 3
+  };
+
+  // struct for storing contact data
+
+  struct ContactSurf {
+    int index, neigh_index, type, flag, nside, exposed, concave_contact;
+    double overlap, overlap_ext, overlap_force;
+    double weight_ext, weight_convex, weight_overlap, weight_contribution;
+    double contact[3], dr[3], surf_norm[3], force_norm[3], dr_ext[3];
+  };
+
+  FixSurface(class LAMMPS *, int, char **);
+  ~FixSurface() override;
+
+  virtual int setmask() = 0;
+
+  virtual void post_constructor() {}
+
+ protected:
+
+  // surfs read from molecule or STL files
+
+  struct Point {
+    double x[3];
+  };
+
+  struct Line {
+    int mol,type;           // molID and type of the line
+    int p1,p2;              // indices of points in line segment
+    double norm[3];         // unit normal to line = Z x (p2-p1)
+  };
+
+  struct Tri {
+    int mol,type;           // modID and type of the triangle
+    int p1,p2,p3;           // indices of points in triangle
+    double norm[3];         // unit normal to tri plane = (p2-p1) x (p3-p1)
+  };
+
+  // methods common to both global and local surfs
+
+  void extract_from_molecule(char *, std::map<std::tuple<double,double,double>,int> *,
+                             int &, int &, Point *&,
+                             int &, Line *&, int &, Tri *&);
+  void extract_from_stlfile(char *, int, std::map<std::tuple<double,double,double>,int> *,
+                            int &, int &, Point *&, int &, Tri *&);
+
+  void connectivity2d_global(int, int, Line *, Connect2d *&, int **&, int **&);
+  int connectivity3d_global(int, int, Tri *, Connect3d *&,
+                            int **&, int **&, int **&,
+                            int **&, int **&, int **&);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif

src/GRANSURF/fix_surface_global.h

@@ -0,0 +1,244 @@
+/* -*- 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(surface/global,FixSurfaceGlobal)
+// clang-format on
+#else
+
+#ifndef LMP_FIX_SURFACE_GLOBAL_H
+#define LMP_FIX_SURFACE_GLOBAL_H
+
+#include <stdio.h>
+#include "fix_surface.h"
+#include <map>
+#include <unordered_set>
+#include <vector>
+
+namespace LAMMPS_NS {
+
+namespace Granular_NS {
+  class GranularModel;
+}
+
+class FixSurfaceGlobal : public FixSurface {
+ public:
+
+  // neighbor lists for spheres with surfs and shear history
+  // accessed by fix shear/history
+
+  class NeighList *list;
+  class NeighList *listhistory;
+
+  FixSurfaceGlobal(class LAMMPS *, int, char **);
+  ~FixSurfaceGlobal();
+  int setmask();
+  void post_constructor();
+
+  void init() override;
+  void setup_pre_neighbor() override;
+  void initial_integrate(int) override;
+  void pre_neighbor() override;
+  void post_force(int) override;
+
+  int modify_param(int, char **x) override;
+  void reset_dt() override;
+  double memory_usage() override;
+
+  void *extract(const char *, int &) override;
+  int image(int *&, double **&) override;
+
+ private:
+  int dimension,firsttime,use_history;
+  double dt,skin;
+  double flatthresh;
+  double Twall;
+  int tvar;
+  char *tstr;
+
+  // per-surf properties
+
+  int maxsurftype;
+  double **xsurf,**vsurf,**omegasurf,*radsurf;
+
+  // granular models
+
+  struct ModelTypes {
+    int plo,phi;
+    int slo,shi;
+  };
+
+  ModelTypes *modeltypes;
+  class Granular_NS::GranularModel **models;   // list of command-line models
+  class Granular_NS::GranularModel ***types2model;  // model assigned to each particle/surf type pair
+
+  int nmodel, maxmodel;
+  int history, size_history, heat_flag;
+
+  // neighbor params
+
+  double triggersq;
+
+  // settings for motion applied to specific surf types
+
+  struct Motion {
+    int active;
+    int mstyle;
+    int vxflag,vyflag,vzflag;
+    int axflag,ayflag,azflag;
+    int xvar,yvar,zvar;
+    int vxvar,vyvar,vzvar;
+    double vx,vy,vz;
+    double ax,ay,az;
+    double dx,dy,dz;
+    double period;
+    double point[3],axis[3],unit[3];
+    double omega;
+    char *xvarstr,*yvarstr,*zvarstr;
+    char *vxvarstr,*vyvarstr,*vzvarstr;
+    double time_origin;
+  };
+
+  struct Motion *motions;  // list of defined motions, can be flagged inactive
+  int nmotion,maxmotion;   // # of defined motions versus allocated size
+  int anymove;             // 1 if any surf motion is enabled
+  int anymove_variable;    // 1 if any surf motion is style VARIABLE
+
+  int *type2motion;        // assingment of surf types (1 to Ntype) to motions
+                           // -1 = non-moving surf type
+
+  double **points_original,**xsurf_original;
+  double **points_lastneigh;
+  int *pointmove;
+
+  // storage of granular history info
+
+  class FixNeighHistory *fix_history;
+  double *zeroes;
+
+  // rigid body masses for use in granular interactions
+
+  class Fix *fix_rigid;    // ptr to rigid body fix, NULL if none
+  double *mass_rigid;      // rigid mass for owned+ghost atoms
+  int nmax;                // allocated size of mass_rigid
+
+  // data structs for extracting surfs from molecule or STL files
+
+  Point *points;              // global list of unique points
+  Line *lines;                // global list of lines
+  Tri *tris;                  // global list of tris
+  int npoints,nlines,ntris;   // count of each
+  int nedges;                 // count of unique tri edges
+  int maxpoints;              // allocated length of points
+  int nsurf;                  // count of lines or tris for 2d/3d
+
+  // ragged 2d arrays for 2d connectivity
+
+  int **neigh_p1;             // indices of other lines connected to endpt 1
+  int **pwhich_p1;            // which point (0/1) on other line is endpt 1
+  int **nside_p1;             // consistency of other line normal
+                              //   SAME_SIDE or OPPOSITE_SIDE
+  int **aflag_p1;             // is this line + other line a FLAT,CONCAVE,CONVEX surf
+                              //   surf = on normal side of this line
+  int **neigh_p2;             // ditto for connections to endpt 2
+  int **pwhich_p2;            // ditto for endpt 2
+  int **nside_p2;             // ditto for endpt 2
+  int **aflag_p2;             // ditto for endpt 2
+
+  // ragged 2d arrays for 3d edge connectivity
+
+  int **neigh_e1;             // indices of other tris connected to edge 1
+  int **ewhich_e1;            // which edge (0/1/2) on other tri is edge 1
+  int **nside_e1;             // consistency of other tri normal
+                              //   SAME_SIDE or OPPOSITE_SIDE
+  int **aflag_e1;             // is this tri + other tri a FLAT,CONCAVE,CONVEX surf
+                              //   surf = on normal side of this tri
+  int **neigh_e2;             // ditto for connections to edge 2
+  int **ewhich_e2;            // ditto for edge 2
+  int **nside_e2;             // ditto for edge 2
+  int **aflag_e2;             // ditto for edge 2
+  int **neigh_e3;             // ditto for connections to edge 3
+  int **ewhich_e3;            // ditto for edge 3
+  int **nside_e3;             // ditto for edge 3
+  int **aflag_e3;             // ditto for edge 3
+
+  // ragged 2d arrays for 3d corner connectivity
+
+  int **neigh_c1;             // indices of other tris connected to cpt 1
+  int **cwhich_c1;            // which corner point (0/1/2) on other tri is cpt 1
+  int **nside_c1;             // consistency of other tri normal
+                              //   SAME_SIDE or OPPOSITE_SIDE, only meaningful for FLAT
+  int **aflag_c1;             // is this tri + other tri a FLAT or CONCAVE surf
+                              //   surf = on normal side of this tri
+  int **neigh_c2;             // indices of other tris connected to cpt 21
+  int **cwhich_c2;            // which corner point (0/1/2) on other tri is cpt 2
+  int **nside_c2;             // ditto for corner 2
+  int **aflag_c2;             // ditto for corner 2
+  int **neigh_c3;             // indices of tris connected to cpt 3
+  int **cwhich_c3;            // which corner point (0/1/2) on other tri is cpt 3
+  int **nside_c3;             // ditto for corner 3
+  int **aflag_c3;             // ditto for corner 3
+
+  // per-surface 2d/3d connectivity
+
+  Connect2d *connect2d;       // 2d connection info
+  Connect3d *connect3d;       // 3d connection info
+
+  class ContactSurf *contact_surfs;
+  int nmax_contact_surfs;
+
+  // data for DumpImage
+
+  int *imflag;
+  double **imdata;
+  int imax;
+
+  // private methods
+
+  void check2d();
+  void check3d();
+  void connectivity2d_complete();
+  void connectivity3d_complete();
+  void check_molecules();
+  void stats2d();
+  void stats3d();
+
+  void surface_attributes();
+  void surface_connectivity_attributes();
+
+  // contact processing and force calculation
+
+  void prewalk_connections2d(int, int, std::unordered_set<int> *, std::map<int, int> *);
+  void prewalk_connections3d(int, int, std::vector<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void walk_connections2d(int, std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void walk_connections3d(int, std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void adjust_external_corner(int, int, int, int);
+  void calculate_2d_forces(std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *);
+  void calculate_3d_forces(std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *);
+
+  // surface movement
+
+  int modify_param_move(Motion *, int, char **);
+  void move_linear(int, int);
+  void move_wiggle(int, int);
+  void move_rotate(int, int);
+  void move_transrotate(int, int);
+  void move_rotate_point(int, double *, double *, double, double);
+  void move_variable(int, int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/GRANSURF/fix_surface_local.h

@@ -0,0 +1,223 @@
+/* -*- 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
+
+FixStyle(surface/local,FixSurfaceLocal)
+
+#else
+
+#ifndef LMP_FIX_SURFACE_LOCAL_H
+#define LMP_FIX_SURFACE_LOCAL_H
+
+#include <stdio.h>
+#include "fix_surface.h"
+#include <map>
+#include "my_pool_chunk.h"
+
+namespace LAMMPS_NS {
+
+class FixSurfaceLocal : public FixSurface {
+ public:
+
+  // 2d/3d connectivity
+
+  Connect2d *connect2d;         // 2d connection info
+  Connect3d *connect3d;         // 3d connection info
+  int nmax_connect;             // allocated size of connect2d/3d
+
+  FixSurfaceLocal(class LAMMPS *, int, char **);
+  virtual ~FixSurfaceLocal();
+  int setmask();
+  void post_constructor();
+
+  void setup_pre_neighbor() override;
+  void pre_neighbor() override;
+
+  void grow_arrays(int) override;
+  void grow_connect();
+  void copy_arrays(int, int, int) override;
+  void set_arrays(int) override;
+  void clear_bonus() override;
+
+  int pack_border(int, int *, double *) override;
+  int unpack_border(int, int, double *) override;
+  int pack_exchange(int, double *) override;
+  int unpack_exchange(int, double *) override;
+  int pack_forward_comm(int, int *, double *, int, int *) override;
+  void unpack_forward_comm(int, int, double *) override;
+
+  double memory_usage() override;
+
+ private:
+  int dimension,mode;
+  double flatthresh;
+  double Twall;
+  int tvar;
+  char *tstr;
+
+  int ninput;
+  int *input_modes,*input_stypes;
+  char **input_sources;
+
+  int flag_complete;    // whether one-time connectivity info has been calculated
+
+  class AtomVecLine *avec_line;
+  class AtomVecTri *avec_tri;
+
+  // memory allocation for tagint and int vectors in Connect 2d/3d
+
+  MyPoolChunk<int> *ipc;        // allocator for most 2d/3d connectivity vecs
+  MyPoolChunk<tagint> *tpc;     // allocator for tagint 2d/3d connectivity vecs
+
+  struct Pool2d {
+    int neigh_p1,neigh_p2;    // pool indices of neigh_p12 chunks
+    int pwhich_p1,pwhich_p2;  // pool indices of pwhich_p12 chunks
+    int nside_p1,nside_p2;    // pool indices of nside_p12 chunks
+    int aflag_p1,aflag_p2;    // pool indices of aflag_p12 chunks
+  };
+
+  struct Pool3d {
+    int neigh_e1,neigh_e2,neigh_e3;     // pool indices of neigh_e123 chunks
+    int ewhich_e1,ewhich_e2,ewhich_e3;  // pool indices of neigh_e123 chunks
+    int nside_e1,nside_e2,nside_e3;     // pool indices of neigh_e123 chunks
+    int aflag_e1,aflag_e2,aflag_e3;     // pool indices of neigh_e123 chunks
+    int neigh_c1,neigh_c2,neigh_c3;     // pool indices of neigh_c123 chunks
+    int cwhich_c1,cwhich_c2,cwhich_c3;  // pool indices of neigh_c123 chunks
+    int nside_c1,nside_c2,nside_c3;     // pool indices of neigh_c123 chunks
+    int aflag_c1,aflag_c2,aflag_c3;     // pool indices of neigh_c123 chunks
+  };
+
+  Pool2d *pool2d;               // pool indices of connect2d vectors
+  Pool3d *pool3d;               // pool indices of connect3d vectors
+
+  int *atom2connect;       // per-atom index into connect 2d/3d vecs, -1 if none
+  int *connect2atom;       // per-connect index into atoms
+
+  // ragged 2d arrays for 2d connectivity for global case
+
+  tagint **neigh_p1,**neigh_p2;
+
+  // ragged 2d arrays for 3d connectivity for global case
+
+  tagint **neigh_e1,**neigh_e2,**neigh_e3;
+  tagint **neigh_c1,**neigh_c2,**neigh_c3;
+
+  // size of local/ghost connection info vectors
+
+  int nlocal_connect,nghost_connect;
+
+  // data structs for calculating global connectivity of line/tri particles
+  // only used by Rvous comm during setup
+
+  struct InRvous {            // datum for each bin of each endpt in each line
+    int proc;                 // owning proc
+    int ibin;                 // bin assignment
+    int ilocal;               // index of line/tri particle
+    int ipoint;               // 0/1 for line endpt, 0/1/2 for tri corner pt
+    tagint atomID;            // ID of line/tri particle
+    double x[3];              // coords of endpt or corner pt
+  };
+
+  struct OutRvous {           // datum returned to owning proc
+    int ilocal;               // index of line/tri particle
+    int ipoint;               // 0/1 for line endpt, 0/1/2 for tri corner pt
+    tagint atomID;            // ID of other line/tri particle with matching point
+  };
+
+  double bboxlo[3],bboxhi[3];    // bounding box around all lines/tris
+
+  // data structs for extracting surfs from molecule template or STL file
+  // these are global data structs for all surfs, including connectivity
+  // only used during setup, then deleted
+
+  Point *points;              // global list of points
+  Line *lines;                // global list of lines
+  Tri *tris;                  // global list of tris
+  int npoints,nlines,ntris;   // count of each
+  int maxpoints;
+
+  Connect2d *connect2dall;    // global connectivity info
+  Connect3d *connect3dall;
+
+  int **plines;               // ragged 2d array for global line end pt lists
+  int **etris;                // ragged 2d array for global tri edge lists
+  int **ctris;                // ragged 2d array for global tri corner pt lists
+
+  struct OnePt {               // one end/corner point of iline/itri in a bin
+    int iatom;                 // local index of the line/tri in atom list
+    int iconnect;              // local index of the line/tri in connect list
+    int ptwhich;               // 1/2 for two end pts of line
+                               // 1/2/3 for three corner pts of tri
+  };
+
+  OnePt *pts;                      // list of pts in all bins
+  int *bincount;                   // # of pts per bin
+  int *binfirst;                   // index into pts of first pt in bin
+  int nbins,nbinx,nbiny,nbinz;     // # of total bins and in each dim
+  double invbinx,invbiny,invbinz;  // inverse of bin size
+  double binlo[3],binhi[3];        // bounds of region that is binned
+
+  double eps,epssq;            // distance tolerance for matching 2 points
+                               // for different lines/tris to be connected
+
+  int nmatch;                  // # of line connections
+  int nmatch1,nmatch2;         // # of tri connections
+  int errormatch;              // # of errors with line connectivity
+  int errormatch1,errormatch2; // # of errors with tri connectivity
+
+  int vecflag;            // 0/1 whether tri matching should also
+                          // store variable-length vecs of corner connections
+
+  // static variable for Rvous communication callback to access class data
+  // callback functions for Rvous communication
+
+  static FixSurfaceLocal *fptr;
+  static void linematch(int, char *);
+  static void trimatch(int, char *);
+  static int point_match(int, char *, int &, int *&, char *&, void *);
+
+  // private methods
+
+  // local connectivity build from line or triangle particles
+
+  void connectivity2d_local();
+  void connectivity3d_local();
+  void calculate_endpts(double **);
+  int overlap_bins_2d(double *, double, int *);
+  void calculate_corners(double **);
+  int overlap_bins_3d(double *, double, int *);
+
+  // global connectivity build from molecule or STL files
+
+  int check_exist();
+  void assign2d();
+  void assign3d();
+
+  // finish the connectivity build for both local and global cases
+
+  void connectivity2d_complete();
+  void connectivity3d_complete();
+  int same_point(double *, double *);
+  void epsilon_calculate();
+
+  void check2d();
+  void check3d();
+  void stats2d();
+  void stats3d();
+};
+
+}
+
+#endif
+#endif

src/GRANSURF/pair_line_gran_hooke.cpp

@@ -0,0 +1,284 @@
+/* -*- 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 "pair_line_gran_hooke.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairLineGranHooke::PairLineGranHooke(LAMMPS *lmp) :
+  PairLineGranHookeHistory(lmp)
+{
+  history = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLineGranHooke::compute(int eflag, int vflag)
+{
+  int i,j,k,ii,jj,inum,jnum,jflag,kflag,otherflag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
+  double radi,radj,radsum,rsq,r,rinv,rsqinv;
+  double factor_couple;
+  double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
+  double wr1,wr2,wr3;
+  double vtr1,vtr2,vtr3,vrel;
+  double mi,mj,meff,mline;
+  double damp,ccel,tor1,tor2,tor3;
+  double fn,fs,ft,fs1,fs2,fs3;
+  double dr[3],ds[3],vline[3],contact[3];
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  // if just reneighbored:
+  // update rigid body masses for owned/ghost atoms if using FixRigid
+  //   body[i] = which body atom I is in, -1 if none
+  //   mass_body = mass of each rigid body
+  // forward comm mass_rigid so have it for ghost lines
+
+  if (neighbor->ago == 0) {
+    if (fix_rigid) {
+      int tmp;
+      int *body = (int *) fix_rigid->extract("body",tmp);
+      double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
+      if (atom->nmax > nmax) {
+        memory->destroy(mass_rigid);
+        nmax = atom->nmax;
+        memory->create(mass_rigid,nmax,"line/gran:mass_rigid");
+      }
+      int nlocal = atom->nlocal;
+      for (i = 0; i < nlocal; i++) {
+        if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
+        else mass_rigid[i] = 0.0;
+      }
+      comm->forward_comm(this);
+    }
+
+    connect2d = fsl->connect2d;
+  }
+
+  // pre-calculate current end pts of owned+ghost lines
+  // only once per reneighbor if surfs not moving
+
+  if (surfmoveflag || neighbor->ago == 0) calculate_endpts();
+
+  // loop over neighbors of my atoms
+  // I is always sphere, J is always line
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double *radius = atom->radius;
+  double *rmass = atom->rmass;
+  tagint *tag = atom->tag;
+  int *line = atom->line;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    radi = radius[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      radj = radius[j];
+      radsum = radi + radj;
+
+      if (rsq < radsum*radsum) {
+
+        // sanity check that neighbor list is built correctly
+
+        if (line[i] >= 0 || line[j] < 0)
+          error->one(FLERR,"Pair line/gran iteraction is invalid");
+
+        // check for overlap of sphere and line segment
+        // jflag = 0 for no overlap, 1 for interior line pt, -1/-2 for end pts
+        // if no overlap, just continue
+        // for overlap, also return:
+        //   contact = nearest point on line to sphere center
+        //   dr = vector from contact pt to sphere center
+        //   rsq = squared length of dr
+
+        jflag = overlap_sphere_line(i,j,contact,dr,rsq);
+
+        if (!jflag) continue;
+
+        // if contact = line end pt:
+        // check overlap status of line adjacent to the end pt
+        // otherflag = 0/1 for this/other line performs calculation
+
+        if (jflag < 0) {
+          otherflag = endpt_neigh_check(i,j,jflag);
+          if (otherflag) continue;
+        }
+
+        //printf("CONTACT %ld: %d %d: %d %d\n",update->ntimestep,i,j,
+        //      tag[i],tag[j]);
+
+        // NOTE: add logic to check for coupled contacts and weight them
+
+        factor_couple = 1.0;
+
+        // ds = vector from line center to contact pt
+
+        r = sqrt(rsq);
+        rinv = 1.0/r;
+        rsqinv = 1.0/rsq;
+
+        ds[0] = contact[0] - x[j][0];
+        ds[1] = contact[1] - x[j][1];
+        ds[2] = contact[2] - x[j][2];
+
+        // vline = velocity of contact pt on line, translation + rotation
+
+        vline[0] = v[j][0] + (omega[j][1]*ds[2] - omega[j][2]*ds[1]);
+        vline[1] = v[j][1] + (omega[j][2]*ds[0] - omega[j][0]*ds[2]);
+        vline[2] = v[j][2] + (omega[j][0]*ds[1] - omega[j][1]*ds[0]);
+
+        // relative translational velocity
+
+        vr1 = v[i][0] - vline[0];
+        vr2 = v[i][1] - vline[1];
+        vr3 = v[i][2] - vline[2];
+
+        // normal component
+
+        vnnr = vr1*dr[0] + vr2*dr[1] + vr3*dr[2];
+        vn1 = dr[0]*vnnr * rsqinv;
+        vn2 = dr[1]*vnnr * rsqinv;
+        vn3 = dr[2]*vnnr * rsqinv;
+
+        // tangential component
+
+        vt1 = vr1 - vn1;
+        vt2 = vr2 - vn2;
+        vt3 = vr3 - vn3;
+
+        // relative rotational velocity
+
+        wr1 = (radi*omega[i][0]) * rinv;
+        wr2 = (radi*omega[i][1]) * rinv;
+        wr3 = (radi*omega[i][2]) * rinv;
+
+        // meff = effective mass of sphere and line
+        // if I or J is part of rigid body, use body mass
+        // if line is not part of rigid body assume infinite mass
+
+        meff = rmass[i];
+        if (fix_rigid) {
+          if (mass_rigid[i] > 0.0) meff = mass_rigid[i];
+          if (mass_rigid[j] > 0.0) {
+            mline = mass_rigid[j];
+            meff = meff*mline / (meff+mline);
+          }
+        }
+
+        // normal forces = Hookian contact + normal velocity damping
+
+        damp = meff*gamman*vnnr*rsqinv;
+        ccel = kn*(radi-r)*rinv - damp;
+        ccel *= factor_couple;
+
+        // relative velocities
+
+        vtr1 = vt1 - (dr[2]*wr2-dr[1]*wr3);
+        vtr2 = vt2 - (dr[0]*wr3-dr[2]*wr1);
+        vtr3 = vt3 - (dr[1]*wr1-dr[0]*wr2);
+        vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+        vrel = sqrt(vrel);
+
+        // force normalization
+
+        fn = xmu * fabs(ccel*r);
+        fs = meff*gammat*vrel;
+        if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
+        else ft = 0.0;
+
+        // tangential force due to tangential velocity damping
+
+        fs1 = -ft*vtr1 * factor_couple;
+        fs2 = -ft*vtr2 * factor_couple;
+        fs3 = -ft*vtr3 * factor_couple;
+
+        // total force on sphere
+
+        fx = dr[0]*ccel + fs1;
+        fy = dr[1]*ccel + fs2;
+        fz = dr[2]*ccel + fs3;
+
+        // sphere force & torque
+
+        f[i][0] += fx;
+        f[i][1] += fy;
+        f[i][2] += fz;
+
+        tor1 = rinv * (dr[1]*fs3 - dr[2]*fs2);
+        tor2 = rinv * (dr[2]*fs1 - dr[0]*fs3);
+        tor3 = rinv * (dr[0]*fs2 - dr[1]*fs1);
+        torque[i][0] -= radi*tor1;
+        torque[i][1] -= radi*tor2;
+        torque[i][2] -= radi*tor3;
+
+        // line force & torque
+        // torque applied at contact pt
+        // use total force for torque
+        //   since opposite force is not norm/tang to line at its end pt
+
+        f[j][0] -= fx;
+        f[j][1] -= fy;
+        f[j][2] -= fz;
+
+        torque[j][0] -= ds[1]*fz - ds[2]*fy;
+        torque[j][1] -= ds[2]*fx - ds[0]*fz;
+        torque[j][2] -= ds[0]*fy - ds[1]*fx;
+
+        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+                                 0.0,0.0,fx,fy,fz,dr[0],dr[1],dr[2]);
+      }
+    }
+  }
+
+  // NOTE: should there be virial contributions from boundary tris?
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}

src/GRANSURF/pair_line_gran_hooke.h

@@ -0,0 +1,37 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(line/gran/hooke,PairLineGranHooke)
+
+#else
+
+#ifndef LMP_PAIR_LINE_GRAN_HOOKE_H
+#define LMP_PAIR_LINE_GRAN_HOOKE_H
+
+#include "pair_line_gran_hooke_history.h"
+
+namespace LAMMPS_NS {
+
+class PairLineGranHooke : public PairLineGranHookeHistory {
+ public:
+  PairLineGranHooke(class LAMMPS *);
+  ~PairLineGranHooke() {}
+  void compute(int, int);
+};
+
+}
+
+#endif
+#endif

src/GRANSURF/pair_line_gran_hooke_history.cpp

@@ -0,0 +1,961 @@
+/* -*- 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 "pair_line_gran_hooke_history.h"
+
+#include "atom.h"
+#include "atom_vec_line.h"
+#include "comm.h"
+#include "error.h"
+#include "fix.h"
+#include "fix_dummy.h"
+#include "fix_neigh_history.h"
+#include "fix_surface_local.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairLineGranHookeHistory::PairLineGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
+{
+  single_enable = 0;
+  history = 1;
+  size_history = 3;
+
+  nmax = 0;
+  mass_rigid = nullptr;
+
+  emax = 0;
+  endpts = nullptr;
+
+  // set comm size needed by this Pair if used with fix rigid
+
+  comm_forward = 1;
+
+  // create dummy fix as placeholder for FixNeighHistory
+  // this is so final order of Modify:fix will conform to input script
+
+  fix_history = nullptr;
+  fix_dummy = dynamic_cast<FixDummy *>(
+      modify->add_fix("NEIGH_HISTORY_HHLINE_DUMMY" + std::to_string(instance_me) + " all DUMMY"));
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLineGranHookeHistory::~PairLineGranHookeHistory()
+{
+  delete [] svector;
+
+  if (!fix_history)
+    modify->delete_fix("NEIGH_HISTORY_HHLINE_DUMMY" + std::to_string(instance_me));
+  else
+    modify->delete_fix("NEIGH_HISTORY_HHLINE" + std::to_string(instance_me));
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    delete [] onerad_dynamic;
+    delete [] onerad_frozen;
+    delete [] maxrad_dynamic;
+    delete [] maxrad_frozen;
+  }
+
+  memory->destroy(mass_rigid);
+  memory->destroy(endpts);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::compute(int eflag, int vflag)
+{
+  int i,j,k,ii,jj,inum,jnum,jflag,kflag,otherflag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
+  double radi,radj,radsum,rsq,r,rinv,rsqinv;
+  double factor_couple;
+  double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
+  double wr1,wr2,wr3;
+  double vtr1,vtr2,vtr3,vrel;
+  double mi,mj,meff,mline;
+  double damp,ccel,tor1,tor2,tor3;
+  double fn,fs,ft,fs1,fs2,fs3;
+  double shrmag,rsht;
+  double dr[3],ds[3],vline[3],contact[3];
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *touch,**firsttouch;
+  double *shear,*allshear,**firstshear;
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  int shearupdate = 1;
+  if (update->setupflag) shearupdate = 0;
+
+  // if just reneighbored:
+  // update rigid body info for owned & ghost atoms if using FixRigid masses
+  // body[i] = which body atom I is in, -1 if none
+  // mass_body = mass of each rigid body
+  // forward comm mass_rigid so have it for ghost lines
+  // also grab current line connectivity info from FixSurfaceLocal
+
+  if (neighbor->ago == 0) {
+    if (fix_rigid) {
+      int tmp;
+      int *body = (int *) fix_rigid->extract("body",tmp);
+      double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
+      if (atom->nmax > nmax) {
+        memory->destroy(mass_rigid);
+        nmax = atom->nmax;
+        memory->create(mass_rigid,nmax,"line/gran:mass_rigid");
+      }
+      int nlocal = atom->nlocal;
+      for (i = 0; i < nlocal; i++)
+        if (body[i] >= 0)
+          mass_rigid[i] = mass_body[body[i]];
+        else
+          mass_rigid[i] = 0.0;
+      comm->forward_comm(this);
+    }
+
+    connect2d = fsl->connect2d;
+  }
+
+  // pre-calculate current end pts of owned+ghost lines
+  // only once per reneighbor if surfs not moving
+
+  if (surfmoveflag || neighbor->ago == 0) calculate_endpts();
+
+  // loop over neighbors of my atoms
+  // I is always sphere, J is always line
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double *radius = atom->radius;
+  double *rmass = atom->rmass;
+  tagint *tag = atom->tag;
+  int *line = atom->line;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+  firsttouch = fix_history->firstflag;
+  firstshear = fix_history->firstvalue;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    radi = radius[i];
+    touch = firsttouch[i];
+    allshear = firstshear[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      radj = radius[j];
+      radsum = radi + radj;
+
+      /*
+      if (touch[jj]) {
+        shear = &allshear[3*jj];
+        printf("PRE step %ld ij %d %d shear %g %g %g\n",
+               update->ntimestep,atom->tag[i],tag[j],
+               shear[0],shear[1],shear[2]);
+      }
+      */
+
+      if (rsq >= radsum*radsum) {
+
+        // unset non-touching neighbors
+        // do same below if sphere/line are not overlapping
+
+        touch[jj] = 0;
+        shear = &allshear[3*jj];
+        shear[0] = 0.0;
+        shear[1] = 0.0;
+        shear[2] = 0.0;
+
+      } else {
+
+        // sanity check that neighbor list is built correctly
+
+        if (line[i] >= 0 || line[j] < 0)
+          error->one(FLERR,"Pair line/gran iteraction is invalid");
+
+        // check for overlap of sphere and line segment
+        // jflag = 0 for no overlap, 1 for interior line pt, -1/-2 for end pts
+        // if no overlap, just continue
+        // for overlap, also return:
+        //   contact = nearest point on line to sphere center
+        //   dr = vector from contact pt to sphere center
+        //   rsq = squared length of dr
+
+        jflag = overlap_sphere_line(i,j,contact,dr,rsq);
+
+        if (!jflag) {
+          touch[jj] = 0;
+          shear = &allshear[3*jj];
+          shear[0] = 0.0;
+          shear[1] = 0.0;
+          shear[2] = 0.0;
+          continue;
+        }
+
+        // if contact = line end pt:
+        // check overlap status of line adjacent to the end pt
+        // otherflag = 0/1 for this/other line performs calculation
+
+        if (jflag < 0) {
+          otherflag = endpt_neigh_check(i,j,jflag);
+          if (otherflag) continue;
+        }
+
+        // NOTE: add logic to persist shear history if contact has changed
+
+        // NOTE: add logic to check for coupled contacts and weight them
+
+        factor_couple = 1.0;
+
+        // ds = vector from line center to contact pt
+
+        r = sqrt(rsq);
+        rinv = 1.0/r;
+        rsqinv = 1.0/rsq;
+
+        ds[0] = contact[0] - x[j][0];
+        ds[1] = contact[1] - x[j][1];
+        ds[2] = contact[2] - x[j][2];
+
+        // vline = velocity of contact pt on line, translation + rotation
+
+        vline[0] = v[j][0] + (omega[j][1]*ds[2] - omega[j][2]*ds[1]);
+        vline[1] = v[j][1] + (omega[j][2]*ds[0] - omega[j][0]*ds[2]);
+        vline[2] = v[j][2] + (omega[j][0]*ds[1] - omega[j][1]*ds[0]);
+
+        // relative translational velocity
+
+        vr1 = v[i][0] - vline[0];
+        vr2 = v[i][1] - vline[1];
+        vr3 = v[i][2] - vline[2];
+
+        // normal component
+
+        vnnr = vr1*dr[0] + vr2*dr[1] + vr3*dr[2];
+        vn1 = dr[0]*vnnr * rsqinv;
+        vn2 = dr[1]*vnnr * rsqinv;
+        vn3 = dr[2]*vnnr * rsqinv;
+
+        // tangential component
+
+        vt1 = vr1 - vn1;
+        vt2 = vr2 - vn2;
+        vt3 = vr3 - vn3;
+
+        // relative rotational velocity
+
+        wr1 = (radi*omega[i][0]) * rinv;
+        wr2 = (radi*omega[i][1]) * rinv;
+        wr3 = (radi*omega[i][2]) * rinv;
+
+        // meff = effective mass of sphere and line
+        // if I or J is part of rigid body, use body mass
+        // if line is not part of rigid body assume infinite mass
+
+        meff = rmass[i];
+        if (fix_rigid) {
+          if (mass_rigid[i] > 0.0) meff = mass_rigid[i];
+          if (mass_rigid[j] > 0.0) {
+            mline = mass_rigid[j];
+            meff = meff*mline / (meff+mline);
+          }
+        }
+
+        // normal forces = Hookian contact + normal velocity damping
+
+        damp = meff*gamman*vnnr*rsqinv;
+        ccel = kn*(radi-r)*rinv - damp;
+        ccel *= factor_couple;
+
+        // relative velocities
+
+        vtr1 = vt1 - (dr[2]*wr2-dr[1]*wr3);
+        vtr2 = vt2 - (dr[0]*wr3-dr[2]*wr1);
+        vtr3 = vt3 - (dr[1]*wr1-dr[0]*wr2);
+        vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+        vrel = sqrt(vrel);
+
+        // shear history effects
+
+        touch[jj] = 1;
+        shear = &allshear[3*jj];
+
+        if (shearupdate) {
+          shear[0] += vtr1*dt;
+          shear[1] += vtr2*dt;
+          shear[2] += vtr3*dt;
+        }
+        shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
+                      shear[2]*shear[2]);
+
+        // rotate shear displacements
+
+        rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
+        rsht *= rsqinv;
+        if (shearupdate) {
+          shear[0] -= rsht*delx;
+          shear[1] -= rsht*dely;
+          shear[2] -= rsht*delz;
+        }
+
+        // tangential force due to tangential velocity damping
+
+        fs1 = - (kt*shear[0] + meff*gammat*vtr1) * factor_couple;;
+        fs2 = - (kt*shear[1] + meff*gammat*vtr2) * factor_couple;;
+        fs3 = - (kt*shear[2] + meff*gammat*vtr3) * factor_couple;;
+
+        // rescale frictional displacements and forces if needed
+
+        fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
+        fn = xmu * fabs(ccel*r);
+
+        if (fs > fn) {
+          if (shrmag != 0.0) {
+            shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
+              meff*gammat*vtr1/kt;
+            shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
+              meff*gammat*vtr2/kt;
+            shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
+              meff*gammat*vtr3/kt;
+            fs1 *= fn/fs;
+            fs2 *= fn/fs;
+            fs3 *= fn/fs;
+          } else fs1 = fs2 = fs3 = 0.0;
+        }
+
+        // total force on sphere
+
+        fx = dr[0]*ccel + fs1;
+        fy = dr[1]*ccel + fs2;
+        fz = dr[2]*ccel + fs3;
+
+        // sphere force & torque
+
+        f[i][0] += fx;
+        f[i][1] += fy;
+        f[i][2] += fz;
+
+        tor1 = rinv * (dr[1]*fs3 - dr[2]*fs2);
+        tor2 = rinv * (dr[2]*fs1 - dr[0]*fs3);
+        tor3 = rinv * (dr[0]*fs2 - dr[1]*fs1);
+        torque[i][0] -= radi*tor1;
+        torque[i][1] -= radi*tor2;
+        torque[i][2] -= radi*tor3;
+
+        // line force & torque
+        // torque applied at contact pt
+        // use total force for torque
+        //   since opposite force is not norm/tang to line at its end pt
+
+        f[j][0] -= fx;
+        f[j][1] -= fy;
+        f[j][2] -= fz;
+
+        torque[j][0] -= ds[1]*fz - ds[2]*fy;
+        torque[j][1] -= ds[2]*fx - ds[0]*fz;
+        torque[j][2] -= ds[0]*fy - ds[1]*fx;
+
+        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+                                 0.0,0.0,fx,fy,fz,dr[0],dr[1],dr[2]);
+      }
+
+      /*
+      if (touch[jj]) {
+        shear = &allshear[3*jj];
+        printf("POST step %ld ij %d %d shear %g %g %g\n",
+               update->ntimestep,atom->tag[i],tag[j],
+               shear[0],shear[1],shear[2]);
+      }
+      */
+
+    }
+  }
+
+  // NOTE: should there be virial contributions from boundary tris?
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  onerad_dynamic = new double[n+1];
+  onerad_frozen = new double[n+1];
+  maxrad_dynamic = new double[n+1];
+  maxrad_frozen = new double[n+1];
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::settings(int narg, char **arg)
+{
+  if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_style command");
+
+  kn = utils::numeric(FLERR,arg[0],false,lmp);
+  if (strcmp(arg[1],"NULL") == 0)
+    kt = kn * 2.0/7.0;
+  else
+    kt = utils::numeric(FLERR,arg[1],false,lmp);
+
+  gamman = utils::numeric(FLERR,arg[2],false,lmp);
+  if (strcmp(arg[3],"NULL") == 0)
+    gammat = 0.5 * gamman;
+  else
+    gammat = utils::numeric(FLERR,arg[3],false,lmp);
+
+  xmu = utils::numeric(FLERR,arg[4],false,lmp);
+  dampflag = utils::inumeric(FLERR,arg[5],false,lmp);
+  if (dampflag == 0) gammat = 0.0;
+
+  limit_damping = 0;
+  if (narg == 7) {
+    if (strcmp(arg[6], "limit_damping") == 0)
+      limit_damping = 1;
+    else
+      error->all(FLERR, "Illegal pair_style command");
+  }
+
+  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 pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::coeff(int narg, char **arg)
+{
+  if (narg > 2) error->all(FLERR,"Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
+  utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::init_style()
+{
+  int i;
+
+  dt = update->dt;
+
+  // error and warning checks
+
+  avec = (AtomVecLine *) atom->style_match("line");
+  if (!avec) error->all(FLERR,"Pair line/gran requires atom style line");
+  if (!atom->radius_flag || !atom->rmass_flag)
+    error->all(FLERR, "Pair line/gran requires atom attributes radius, rmass");
+  if (!force->newton_pair)
+    error->all(FLERR,"Pair style line/gran requires newton pair on");
+  if (comm->ghost_velocity == 0)
+    error->all(FLERR,"Pair line/gran requires ghost atoms store velocity");
+
+  // need a granular neighbor list
+
+  if (history)
+    neighbor->add_request(this,NeighConst::REQ_SIZE | NeighConst::REQ_ONESIDED |
+                          NeighConst::REQ_HISTORY);
+  else
+    neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_ONESIDED);
+
+  // if history is stored and first init, create Fix to store history
+  // it replaces FixDummy, created in the constructor
+  // this is so its order in the fix list is preserved
+
+  if (history && (fix_history == nullptr)) {
+    auto cmd = fmt::format("NEIGH_HISTORY_HHLINE{} all NEIGH_HISTORY {} onesided", instance_me, size_history);
+    fix_history = dynamic_cast<FixNeighHistory *>(
+        modify->replace_fix("NEIGH_HISTORY_HHLINE_DUMMY" + std::to_string(instance_me), cmd, 1));
+    fix_history->pair = this;
+  }
+
+  // set ptr to FixSurfaceLocal for surf connectivity info
+
+  fsl = nullptr;
+  for (int m = 0; m < modify->nfix; m++) {
+    if (strcmp(modify->fix[m]->style,"surface/local") == 0) {
+      if (fsl)
+        error->all(FLERR,"Pair line/gran requires single fix surface/local");
+      fsl = (FixSurfaceLocal *) modify->fix[m];
+    }
+  }
+  if (!fsl) error->all(FLERR,"Pair line/gran requires a fix surface/local");
+
+  // surfmoveflag = 1 if surfs may move at every step
+  // yes if fix move exists and its group includes lines
+  // NOTE: are there other conditions, like fix deform or fix npt?
+
+  surfmoveflag = 0;
+  for (int m = 0; m < modify->nfix; m++) {
+    if (strcmp(modify->fix[m]->style,"move") == 0) {
+      int groupbit = modify->fix[m]->groupbit;
+      int *line = atom->line;
+      int *mask = atom->mask;
+      int nlocal = atom->nlocal;
+      int flag = 0;
+      for (int i = 0; i < nlocal; i++) {
+        if (line[i] < 0) continue;
+        if (mask[i] & groupbit) flag = 1;
+      }
+      int any;
+      MPI_Allreduce(&flag,&any,1,MPI_INT,MPI_SUM,world);
+      if (any) surfmoveflag = 1;
+    }
+  }
+
+  // check for FixFreeze and set freeze_group_bit
+
+  auto fixlist = modify->get_fix_by_style("^freeze");
+  if (fixlist.size() == 0)
+    freeze_group_bit = 0;
+  else if (fixlist.size() > 1)
+    error->all(FLERR, "Only one fix freeze command at a time allowed");
+  else
+    freeze_group_bit = fixlist.front()->groupbit;
+
+  // check for FixRigid so can extract rigid body masses
+
+  fix_rigid = nullptr;
+  for (const auto &ifix : modify->get_fix_list()) {
+    if (ifix->rigid_flag) {
+      if (fix_rigid)
+        error->all(FLERR, "Only one fix rigid command at a time allowed");
+      else
+        fix_rigid = ifix;
+    }
+  }
+
+  // check for FixPour and FixDeposit so can extract particle radii
+
+  auto pours = modify->get_fix_by_style("^pour");
+  auto deps = modify->get_fix_by_style("^deposit");
+
+  // set maxrad_dynamic and maxrad_frozen for each type
+  // include future FixPour and FixDeposit particles as dynamic
+  // lines cannot be frozen
+
+  int itype;
+  for (i = 1; i <= atom->ntypes; i++) {
+    onerad_dynamic[i] = onerad_frozen[i] = 0.0;
+    for (auto &ipour : pours) {
+      itype = i;
+      double maxrad = *((double *) ipour->extract("radius", itype));
+      if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
+    }
+    for (auto &idep : deps) {
+      itype = i;
+      double maxrad = *((double *) idep->extract("radius", itype));
+      if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
+    }
+  }
+
+  double *radius = atom->radius;
+  int *line = atom->line;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+
+  for (i = 0; i < nlocal; i++) {
+    if (line[i] >= 0)
+      onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]);
+    else {
+      if (mask[i] & freeze_group_bit)
+        onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]],radius[i]);
+      else
+        onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]);
+    }
+  }
+
+  MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,
+                MPI_DOUBLE,MPI_MAX,world);
+  MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,
+                MPI_DOUBLE,MPI_MAX,world);
+
+  // set fix which stores history info
+
+  if (history) {
+    fix_history = dynamic_cast<FixNeighHistory *>(
+        modify->get_fix_by_id("NEIGH_HISTORY_HHLINE" + std::to_string(instance_me)));
+    if (!fix_history) error->all(FLERR, "Could not find pair fix neigh history ID");
+  }
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLineGranHookeHistory::init_one(int i, int j)
+{
+  if (!allocated) allocate();
+
+  // cutoff = sum of max I,J radii for
+  // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
+
+  double cutoff = maxrad_dynamic[i]+maxrad_dynamic[j];
+  cutoff = MAX(cutoff,maxrad_frozen[i]+maxrad_dynamic[j]);
+  cutoff = MAX(cutoff,maxrad_dynamic[i]+maxrad_frozen[j]);
+  return cutoff;
+}
+
+/* ----------------------------------------------------------------------
+  proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++)
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+  proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0)
+        utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+    }
+}
+
+/* ----------------------------------------------------------------------
+  proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::write_restart_settings(FILE *fp)
+{
+  fwrite(&kn,sizeof(double),1,fp);
+  fwrite(&kt,sizeof(double),1,fp);
+  fwrite(&gamman,sizeof(double),1,fp);
+  fwrite(&gammat,sizeof(double),1,fp);
+  fwrite(&xmu,sizeof(double),1,fp);
+  fwrite(&dampflag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+  proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::read_restart_settings(FILE *fp)
+{
+  if (comm->me == 0) {
+    utils::sfread(FLERR,&kn,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&kt,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&gamman,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&gammat,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&xmu,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&dampflag,sizeof(int),1,fp,nullptr,error);
+  }
+  MPI_Bcast(&kn,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&kt,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&gamman,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&gammat,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&xmu,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&dampflag,1,MPI_INT,0,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::reset_dt()
+{
+  dt = update->dt;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int PairLineGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
+                                                int pbc_flag, int *pbc)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    buf[m++] = mass_rigid[j];
+  }
+
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::unpack_forward_comm(int n, int first,
+                                                   double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+
+  for (i = first; i < last; i++)
+    mass_rigid[i] = buf[m++];
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double PairLineGranHookeHistory::memory_usage()
+{
+  double bytes = nmax * sizeof(double);
+  bytes = emax*4 * sizeof(double);        // endpts array for line particles
+  return bytes;
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// private methods specific to PairLineGranHookeHistory
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+/* ----------------------------------------------------------------------
+   compute current end points of owned and ghost lines
+   nothing computed for particles that are not lines
+------------------------------------------------------------------------- */
+
+void PairLineGranHookeHistory::calculate_endpts()
+{
+  int i,m;
+  double length,theta,dx,dy;
+  double *endpt;
+
+  // realloc endpts array if necssary
+
+  if (fsl->nmax_connect > emax) {
+    memory->destroy(endpts);
+    emax = fsl->nmax_connect;
+    memory->create(endpts,emax,4,"line/gran:endpts");
+  }
+
+  AtomVecLine::Bonus *bonus = avec->bonus;
+  double **x = atom->x;
+  int *line = atom->line;
+  int n = atom->nlocal + atom->nghost;
+
+  for (i = 0; i < n; i++) {
+    if (line[i] < 0) continue;
+    m = line[i];
+    length = bonus[m].length;
+    theta = bonus[m].theta;
+    dx = 0.5*length*cos(theta);
+    dy = 0.5*length*sin(theta);
+    endpt = endpts[m];
+    endpt[0] = x[i][0] - dx;
+    endpt[1] = x[i][1] - dy;
+    endpt[2] = x[i][0] + dx;
+    endpt[3] = x[i][1] + dy;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute nearest point between sphere I and line segment J
+   return 0 if no contact, 1 if pt is interior to line segment,
+     -1/-2 if pt = line end point 1/2
+   if contact, return:
+     pt = point on line segment
+     r = vector from pt to sphere center
+     rsq = squared length of r
+   based on geometry.cpp::distsq_point_line() in SPARTA
+------------------------------------------------------------------------- */
+
+int PairLineGranHookeHistory::overlap_sphere_line(int i, int j, double *pt,
+                                           double *r, double &rsq)
+{
+  double p1[3],p2[3];
+  double a[3],b[3];
+
+  // P1,P2 = end points of line segment
+
+  double *endpt = endpts[atom->line[j]];
+
+  p1[0] = endpt[0];
+  p1[1] = endpt[1];
+  p1[2] = 0.0;
+  p2[0] = endpt[2];
+  p2[1] = endpt[3];
+  p2[2] = 0.0;
+
+  // A = vector from P1 to Xsphere
+  // B = vector from P1 to P2
+
+  double *xsphere = atom->x[i];
+  MathExtra::sub3(xsphere,p1,a);
+  MathExtra::sub3(p2,p1,b);
+
+  // alpha = fraction of distance from P1 to P2 that P is located at
+  // P = projected point on infinite line that is nearest to Xsphere center
+  // alpha can be any value
+
+  double alpha = MathExtra::dot3(a,b) / MathExtra::lensq3(b);
+
+  // pt = point on line segment that is nearest to Xsphere center
+  // if alpha <= 0.0, pt = P1, ptflag = -1
+  // if alpha >= 1.0, pt = P2, ptflag = -2
+  // else pt = P1 + alpha*(P2-P1), ptflag = 1
+
+  int ptflag;
+  if (alpha <= 0.0) {
+    ptflag = -1;
+    pt[0] = p1[0];
+    pt[1] = p1[1];
+    pt[2] = p1[2];
+  } else if (alpha >= 1.0) {
+    ptflag = -2;
+    pt[0] = p2[0];
+    pt[1] = p2[1];
+    pt[2] = p2[2];
+  } else {
+    ptflag = 1;
+    pt[0] = p1[0] + alpha*b[0];
+    pt[1] = p1[1] + alpha*b[1];
+    pt[2] = p1[2] + alpha*b[2];
+  }
+
+  // R = vector from nearest pt on line to Xsphere center
+  // return ptflag if len(R) < sphere radius
+  // else no contact, return 0
+
+  double radsq = atom->radius[i] * atom->radius[i];
+  MathExtra::sub3(xsphere,pt,r);
+  rsq = MathExtra::lensq3(r);
+  if (rsq < radsq) return ptflag;
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   check overlap status of sphere I with line J versus any neighbor lines K
+   I overlaps J at jflag = -1,-2 for two end points
+   return 0 if this line J performs computation
+   return 1 if some other line K performs computation
+------------------------------------------------------------------------- */
+
+int PairLineGranHookeHistory::endpt_neigh_check(int i, int j, int jflag)
+{
+  // ncheck = # of neighbor lines to check
+  // neighs = indices of neighbor lines (including self)
+
+  int ncheck;
+  int *neighs;
+
+  int jc = atom->line[j];
+  if (jflag == -1) {
+    if (connect2d[jc].np1 == 1) return 0;
+    ncheck = connect2d[jc].np1;
+    neighs = connect2d[jc].neigh_p1;
+  } else if (jflag == -2) {
+    if (connect2d[jc].np2 == 1) return 0;
+    ncheck = connect2d[jc].np2;
+    neighs = connect2d[jc].neigh_p2;
+  }
+
+  // check overlap with each neighbor line
+  // if any line has interior overlap, another line computes
+  // if all lines have endpt overlap, line with lowest ID computes
+  // kflag = overlap status with neighbor line
+  // kflag = 1, interior overlap
+  // kflag = 0, no overlap, should not be possible
+  // kflag < 0, overlap at endpt
+
+  tagint *tag = atom->tag;
+
+  int k,kflag;
+  double rsq;
+  double dr[3],contact[3];
+
+  int linemin = tag[j];
+
+  for (int m = 0; m < ncheck; m++) {
+    if (neighs[m] == tag[j]) continue;     // skip self line
+    k = atom->map(neighs[m]);
+    if (k < 0) error->one(FLERR,"Pair line/gran neighbor line is missing");
+    kflag = overlap_sphere_line(i,k,contact,dr,rsq);
+    if (kflag > 0) return 1;
+    if (kflag == 0) error->one(FLERR,"Fix surface/global neighbor line overlap is invalid");
+    linemin = MIN(linemin,tag[k]);
+  }
+
+  if (tag[j] == linemin) return 0;
+  return 1;
+}

src/GRANSURF/pair_line_gran_hooke_history.h

@@ -0,0 +1,93 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(line/gran/hooke/history,PairLineGranHookeHistory)
+
+#else
+
+#ifndef LMP_PAIR_LINE_GRAN_HOOKE_HISTORY_H
+#define LMP_PAIR_LINE_GRAN_HOOKE_HISTORY_H
+
+#include "pair.h"
+#include "fix_surface_local.h"
+
+namespace LAMMPS_NS {
+
+class PairLineGranHookeHistory : public Pair {
+ public:
+  PairLineGranHookeHistory(class LAMMPS *);
+  virtual ~PairLineGranHookeHistory();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_style();
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void reset_dt();
+  virtual int pack_forward_comm(int, int *, double *, int, int *);
+  virtual void unpack_forward_comm(int, int, double *);
+  double memory_usage();
+
+ protected:
+  double kn,kt,gamman,gammat,xmu;
+  int dampflag,limit_damping;
+  double dt;
+  int freeze_group_bit;
+  int history;
+
+  int neighprev;
+  double *onerad_dynamic,*onerad_frozen;
+  double *maxrad_dynamic,*maxrad_frozen;
+
+  int size_history;
+  int surfmoveflag;
+
+  class FixDummy *fix_dummy;
+  class FixNeighHistory *fix_history;
+
+  int emax;                // allocated size of endpt list
+  double **endpts;         // current end pts of each line
+                           // Nall x 4 array for local + ghost atoms
+
+  // ptr to AtomVec for bonus line info
+
+  class AtomVecLine *avec;
+
+  // line connectivity info for owned and ghost lines
+
+  class FixSurfaceLocal *fsl;              // ptr to surface/local fix
+  FixSurfaceLocal::Connect2d *connect2d;   // ptr to connectivity info
+
+  // storage of rigid body masses for use in granular interactions
+
+  class Fix *fix_rigid;    // ptr to rigid body fix, NULL if none
+  double *mass_rigid;      // rigid mass for owned+ghost atoms
+  int nmax;                // allocated size of mass_rigid
+
+  // local methods
+
+  void allocate();
+  void calculate_endpts();
+  int overlap_sphere_line(int, int, double *, double *, double &);
+  int endpt_neigh_check(int, int, int);
+};
+
+}
+
+#endif
+#endif

src/GRANSURF/pair_surf_granular.h

@@ -0,0 +1,87 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(surf/granular,PairSurfGranular)
+
+#else
+
+#ifndef LMP_PAIR_SURF_GRANULAR_H
+#define LMP_PAIR_SURF_GRANULAR_H
+
+#include "pair_granular.h"
+#include "fix_surface_local.h"
+#include "fix_surface.h"
+#include <map>
+#include <unordered_set>
+#include <vector>
+
+namespace LAMMPS_NS {
+
+class PairSurfGranular : public PairGranular {
+ public:
+  PairSurfGranular(class LAMMPS *);
+  ~PairSurfGranular() override;
+  void compute(int, int) override;
+  void init_style() override;
+  double memory_usage() override;
+
+ protected:
+  int surfmoveflag;
+
+  int style;
+  int emax;                // allocated size of endpt list
+  double **endpts;         // current end pts of each line
+                           // Nall x 6 array for local + ghost atoms
+
+  int cmax;                // allocated size of corners
+  double **corners;        // current corner pts and norm of each tri
+                           // Nall x 12 array for local + ghost atoms
+
+  // ptr to AtomVec for bonus info
+
+  class AtomVecLine *avecline;
+  class AtomVecTri *avectri;
+
+  // line connectivity info for owned and ghost lines
+
+  class FixSurfaceLocal *fsl;              // ptr to surface/local fix
+  FixSurfaceLocal::Connect2d *connect2d;   // ptr to connectivity info
+  FixSurfaceLocal::Connect3d *connect3d;   // ptr to connectivity info
+  MyPoolChunk<int> *tcp;                   // allocator for connectivity info
+
+  class FixSurface::ContactSurf *contact_surfs;
+  int nmax_contact_surfs;
+
+  // lines and tris
+
+  void calculate_endpts();
+  void calculate_corners();
+  void corners2norm(double *, double *);
+
+  // contact processing and force calculation
+
+  void prewalk_connections2d(int, int, std::unordered_set<int> *, std::map<int, int> *);
+  void prewalk_connections3d(int, int, std::vector<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void walk_connections2d(int, std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void walk_connections3d(int, std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::unordered_set<int> *, std::map<int, int> *);
+  void adjust_external_corner(int, int, int, int);
+  void calculate_2d_forces(std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *);
+  void calculate_3d_forces(std::vector<int> *, std::unordered_set<int> *, std::unordered_set<int> *);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/GRANSURF/pair_tri_gran_hooke.cpp

@@ -0,0 +1,286 @@
+/* -*- 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 "pair_tri_gran_hooke.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairTriGranHooke::PairTriGranHooke(LAMMPS *lmp) : PairTriGranHookeHistory(lmp)
+{
+  history = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTriGranHooke::compute(int eflag, int vflag)
+{
+  int i,j,k,ii,jj,inum,jnum,isphere,itri,jflag,kflag,otherflag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
+  double radi,radj,radsum,radsphere,rsq,r,rinv,rsqinv;
+  double factor_couple;
+  double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
+  double wr1,wr2,wr3;
+  double vtr1,vtr2,vtr3,vrel;
+  double mi,mj,meff,mtri;
+  double damp,ccel,tor1,tor2,tor3;
+  double fn,fs,ft,fs1,fs2,fs3;
+  double dr[3],ds[3],vtri[3],contact[3];
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  // if just reneighbored:
+  // update rigid body masses for owned/ghost atoms if using FixRigid
+  //   body[i] = which body atom I is in, -1 if none
+  //   mass_body = mass of each rigid body
+  // forward comm mass_rigid so have it for ghost lines
+
+  if (neighbor->ago == 0) {
+    if (fix_rigid) {
+      int tmp;
+      int *body = (int *) fix_rigid->extract("body",tmp);
+      double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
+      if (atom->nmax > nmax) {
+        memory->destroy(mass_rigid);
+        nmax = atom->nmax;
+        memory->create(mass_rigid,nmax,"line/gran:mass_rigid");
+      }
+      int nlocal = atom->nlocal;
+      for (i = 0; i < nlocal; i++) {
+        if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
+        else mass_rigid[i] = 0.0;
+      }
+      comm->forward_comm(this);
+    }
+
+    connect3d = fsl->connect3d;
+  }
+
+  // pre-calculate current end pts of owned+ghost lines
+  // only once per reneighbor if surfs not moving
+
+  if (surfmoveflag || neighbor->ago == 0) calculate_corners();
+
+  // loop over neighbors of my atoms
+  // I is always sphere, J is always tri
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double *radius = atom->radius;
+  double *rmass = atom->rmass;
+  tagint *tag = atom->tag;
+  int *tri = atom->tri;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    radi = radius[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      radj = radius[j];
+      radsum = radi + radj;
+
+      if (rsq < radsum*radsum) {
+
+        // sanity check that neighbor list is built correctly
+
+        if (tri[i] >= 0 || tri[j] < 0)
+          error->one(FLERR,"Pair tri/gran iteraction is invalid");
+
+        // check for overlap of sphere and triangle
+        // jflag = 0 for no overlap, 1 for interior line pt,
+        //   -1/-2/-3 for 3 edges, -4/-5/-6 for 3 corner pts
+        // if no overlap, just continue
+        // for overlap, also returns:
+        //   contact = nearest point on tri to sphere center
+        //   dr = vector from contact pt to sphere center
+        //   rsq = squared length of dr
+
+        jflag = overlap_sphere_tri(i,j,contact,dr,rsq);
+        if (!jflag) continue;
+
+        // if contact = tri edge or corner:
+        // check status of the tri(s) adjacent to edge or corner
+        // otherflag = 0/1 for this/other tri performs calculation
+
+        if (jflag < 0) {
+          if (jflag >= -3) {
+            otherflag = edge_neigh_check(i,j,jflag);
+            if (otherflag) continue;
+          } else {
+            otherflag = corner_neigh_check(i,j,jflag);
+            if (otherflag) continue;
+          }
+        }
+
+        // NOTE: add logic to check for coupled contacts and weight them
+
+        factor_couple = 1.0;
+
+        // ds = vector from tri center to contact pt
+
+        r = sqrt(rsq);
+        rinv = 1.0/r;
+        rsqinv = 1.0/rsq;
+
+        ds[0] = contact[0] - x[j][0];
+        ds[1] = contact[1] - x[j][1];
+        ds[2] = contact[2] - x[j][2];
+
+        // vtri = velocity of contact pt on tri, translation + rotation
+        // omega for tri was set from angmom by calculate_corners()
+
+        vtri[0] = v[j][0] + (omega[j][1]*ds[2] - omega[j][2]*ds[1]);
+        vtri[1] = v[j][1] + (omega[j][2]*ds[0] - omega[j][0]*ds[2]);
+        vtri[2] = v[j][2] + (omega[j][0]*ds[1] - omega[j][1]*ds[0]);
+
+        // relative translational velocity
+
+        vr1 = v[i][0] - vtri[0];
+        vr2 = v[i][1] - vtri[1];
+        vr3 = v[i][2] - vtri[2];
+
+        // normal component
+
+        vnnr = vr1*dr[0] + vr2*dr[1] + vr3*dr[2];
+        vn1 = dr[0]*vnnr * rsqinv;
+        vn2 = dr[1]*vnnr * rsqinv;
+        vn3 = dr[2]*vnnr * rsqinv;
+
+        // tangential component
+
+        vt1 = vr1 - vn1;
+        vt2 = vr2 - vn2;
+        vt3 = vr3 - vn3;
+
+        // relative rotational velocity
+
+        wr1 = (radi*omega[i][0]) * rinv;
+        wr2 = (radi*omega[i][1]) * rinv;
+        wr3 = (radi*omega[i][2]) * rinv;
+
+        // meff = effective mass of sphere and tri
+        // if I or J is part of rigid body, use body mass
+        // if tri is not part of rigid body assume infinite mass
+
+        meff = rmass[i];
+        if (fix_rigid) {
+          if (mass_rigid[i] > 0.0) meff = mass_rigid[i];
+          if (mass_rigid[j] > 0.0) {
+            mtri = mass_rigid[j];
+            meff = meff*mtri / (meff+mtri);
+          }
+        }
+
+        // normal forces = Hookian contact + normal velocity damping
+
+        damp = meff*gamman*vnnr*rsqinv;
+        ccel = kn*(radi-r)*rinv - damp;
+        ccel *= factor_couple;
+
+        // relative velocities
+
+        vtr1 = vt1 - (dr[2]*wr2-dr[1]*wr3);
+        vtr2 = vt2 - (dr[0]*wr3-dr[2]*wr1);
+        vtr3 = vt3 - (dr[1]*wr1-dr[0]*wr2);
+        vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
+        vrel = sqrt(vrel);
+
+        // force normalization
+
+        fn = xmu * fabs(ccel*r);
+        fs = meff*gammat*vrel;
+        if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
+        else ft = 0.0;
+
+        // tangential force due to tangential velocity damping
+
+        fs1 = -ft*vtr1 * factor_couple;
+        fs2 = -ft*vtr2 * factor_couple;
+        fs3 = -ft*vtr3 * factor_couple;
+
+        // total force on sphere
+
+        fx = dr[0]*ccel + fs1;
+        fy = dr[1]*ccel + fs2;
+        fz = dr[2]*ccel + fs3;
+
+        // sphere force & torque
+
+        f[i][0] += fx;
+        f[i][1] += fy;
+        f[i][2] += fz;
+
+        tor1 = rinv * (dr[1]*fs3 - dr[2]*fs2);
+        tor2 = rinv * (dr[2]*fs1 - dr[0]*fs3);
+        tor3 = rinv * (dr[0]*fs2 - dr[1]*fs1);
+        torque[i][0] -= radi*tor1;
+        torque[i][1] -= radi*tor2;
+        torque[i][2] -= radi*tor3;
+
+        // tri force & torque
+        // torque applied at contact pt
+        // use total force for torque
+        //   since opposite force is not norm/tang to tri at its contact pt
+
+        f[j][0] -= fx;
+        f[j][1] -= fy;
+        f[j][2] -= fz;
+
+        torque[j][0] -= ds[1]*fz - ds[2]*fy;
+        torque[j][1] -= ds[2]*fx - ds[0]*fz;
+        torque[j][2] -= ds[0]*fy - ds[1]*fx;
+
+        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
+                                 0.0,0.0,fx,fy,fz,dr[0],dr[1],dr[2]);
+      }
+    }
+  }
+
+  // NOTE: should there be virial contributions from boundary lines?
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}

src/GRANSURF/pair_tri_gran_hooke.h

@@ -0,0 +1,37 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(tri/gran/hooke,PairTriGranHooke)
+
+#else
+
+#ifndef LMP_PAIR_TRI_GRAN_HOOKE_H
+#define LMP_PAIR_TRI_GRAN_HOOKE_H
+
+#include "pair_tri_gran_hooke_history.h"
+
+namespace LAMMPS_NS {
+
+class PairTriGranHooke : public PairTriGranHookeHistory {
+ public:
+  PairTriGranHooke(class LAMMPS *);
+  ~PairTriGranHooke() {}
+  void compute(int, int);
+};
+
+}
+
+#endif
+#endif

src/GRANSURF/pair_tri_gran_hooke_history.h

@@ -0,0 +1,97 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(tri/gran/hooke/history,PairTriGranHookeHistory)
+
+#else
+
+#ifndef LMP_PAIR_TRI_GRAN_HOOKE_HISTORY_H
+#define LMP_PAIR_TRI_GRAN_HOOKE_HISTORY_H
+
+#include "pair.h"
+#include "fix_surface_local.h"
+#include "my_pool_chunk.h"
+
+namespace LAMMPS_NS {
+
+class PairTriGranHookeHistory : public Pair {
+ public:
+  PairTriGranHookeHistory(class LAMMPS *);
+  virtual ~PairTriGranHookeHistory();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_style();
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void reset_dt();
+  int pack_forward_comm(int, int *, double *, int, int *);
+  void unpack_forward_comm(int, int, double *);
+  double memory_usage();
+
+ protected:
+  double kn,kt,gamman,gammat,xmu;
+  int dampflag,limit_damping;
+  double dt;
+  int freeze_group_bit;
+  int history;
+
+  int neighprev;
+  double *onerad_dynamic,*onerad_frozen;
+  double *maxrad_dynamic,*maxrad_frozen;
+
+  int size_history;
+  int surfmoveflag;
+
+  class FixDummy *fix_dummy;
+  class FixNeighHistory *fix_history;
+
+  int cmax;                // allocated size of corners
+  double **corners;        // current corner pts and norm of each tri
+                           // Nall x 12 array for local + ghost atoms
+
+  // ptr to AtomVec for bonus tri info
+
+  class AtomVecTri *avec;
+
+  // tri connectivity info for owned and ghost tris
+
+  class FixSurfaceLocal *fsl;              // ptr to surface/local fix
+  FixSurfaceLocal::Connect3d *connect3d;   // ptr to connectivity info
+
+  // storage of rigid body masses for use in granular interactions
+
+  class Fix *fix_rigid;    // ptr to rigid body fix, NULL if none
+  double *mass_rigid;      // rigid mass for owned+ghost atoms
+  int nmax;                // allocated size of mass_rigid
+
+  // local methods
+
+  void allocate();
+  void calculate_corners();
+  void corners2norm(double *, double *);
+  int overlap_sphere_tri(int, int, double *, double *, double &);
+  int nearest_point_line(double *, double *, double *, double *);
+  int edge_neigh_check(int, int, int);
+  int corner_neigh_check(int, int, int);
+};
+
+}
+
+#endif
+#endif

src/GRANSURF/surf_extra.cpp

@@ -0,0 +1,298 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   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 "surf_extra.h"
+
+#include "math_extra.h"
+
+using namespace MathExtra;
+
+namespace SurfExtra {
+
+/* ----------------------------------------------------------------------
+   compute nearest point between sphere I and line segment J
+   return 0 if no contact, 1 if pt is interior to line segment,
+     -1/-2 if pt = line end point 1/2
+   if contact, return:
+     pt = point on line segment
+     r = vector from pt to sphere center
+     rsq = squared length of r
+   based on geometry.cpp::distsq_point_line() in SPARTA
+------------------------------------------------------------------------- */
+
+int overlap_sphere_line(double *xsphere, double radius, double *p1, double *p2,
+                        double *pt, double *r, double &rsq)
+{
+  double a[3],b[3];
+
+  // A = vector from P1 to Xsphere
+  // B = vector from P1 to P2
+
+  MathExtra::sub3(xsphere,p1,a);
+  MathExtra::sub3(p2,p1,b);
+
+  // alpha = fraction of distance from P1 to P2 that P is located at
+  // P = projected point on infinite line that is nearest to Xsphere center
+  // alpha can be any value
+
+  double alpha = MathExtra::dot3(a,b) / MathExtra::lensq3(b);
+
+  // pt = point on line segment that is nearest to Xsphere center
+  // if alpha <= 0.0, pt = P1, ptflag = -1
+  // if alpha >= 1.0, pt = P2, ptflag = -2
+  // else pt = P1 + alpha*(P2-P1), ptflag = 1
+
+  int ptflag;
+  if (alpha <= 0.0) {
+    ptflag = -1;
+    pt[0] = p1[0];
+    pt[1] = p1[1];
+    pt[2] = p1[2];
+  } else if (alpha >= 1.0) {
+    ptflag = -2;
+    pt[0] = p2[0];
+    pt[1] = p2[1];
+    pt[2] = p2[2];
+  } else {
+    ptflag = 1;
+    pt[0] = p1[0] + alpha*b[0];
+    pt[1] = p1[1] + alpha*b[1];
+    pt[2] = p1[2] + alpha*b[2];
+  }
+
+  // R = vector from nearest pt on line to Xsphere center
+  // return ptflag if len(R) < sphere radius
+  // else no contact, return 0
+
+  double radsq = radius * radius;
+  MathExtra::sub3(xsphere,pt,r);
+
+  rsq = MathExtra::lensq3(r);
+  if (rsq < radsq) return ptflag;
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   compute nearest point between sphere I and triangle J
+   return 0 if no contact, 1 if pt is interior to triangle,
+     -1/-2/-3 if pt on tri edges, -4/-5/-6 if pt = tri corners 1/2/3
+   if contact, return:
+     pt = point on triangle
+     r = vector from pt to sphere center
+     rsq = squared length of r
+   based on geometry.cpp::distsq_point_tri() in SPARTA
+------------------------------------------------------------------------- */
+
+int overlap_sphere_tri(double *xsphere, double radius,
+                       double *p1, double *p2, double *p3, double *norm,
+                       double *pt, double *r, double &rsq)
+{
+  int e12flag,e23flag,e31flag,o12flag,o23flag,o31flag;
+  int esum,osum,lineflag;
+  double dot;
+  double a[3],point[3],edge[3],pvec[3],xproduct[3];
+
+  // A = vector from P1 to Xsphere
+
+  MathExtra::sub3(xsphere,p1,a);
+
+  // pt = projected point on infinite triangle plane
+
+  double alpha = MathExtra::dot3(a,norm);
+  pt[0] = xsphere[0] - alpha*norm[0];
+  pt[1] = xsphere[1] - alpha*norm[1];
+  pt[2] = xsphere[2] - alpha*norm[2];
+
+  // test if projected point is inside triangle
+  // inside = interior + boundary of tri
+  // edge = edge vector of triangle
+  // pvec = vector from triangle vertex to projected point
+  // xproduct = cross product of edge with pvec
+  // if dot product of xproduct with norm < 0.0 for any of 3 edges,
+  //   projected point is outside tri
+  // NOTE: worry about round-off for pt being on edge or corner?
+
+  int inside = 1;
+  e12flag = e23flag = e31flag = 0;
+  o12flag = o23flag = o31flag = 0;
+
+  MathExtra::sub3(p2,p1,edge);
+  MathExtra::sub3(pt,p1,pvec);
+  MathExtra::cross3(edge,pvec,xproduct);
+  dot = MathExtra::dot3(xproduct,norm);
+  if (dot <= 0.0) {
+    o12flag = 1;
+    if (dot == 0.0) e12flag = 1;
+    else inside = 0;
+  }
+
+  MathExtra::sub3(p3,p2,edge);
+  MathExtra::sub3(pt,p2,pvec);
+  MathExtra::cross3(edge,pvec,xproduct);
+  dot = MathExtra::dot3(xproduct,norm);
+  if (dot <= 0.0) {
+    o23flag = 1;
+    if (dot == 0.0) e23flag = 1;
+    else inside = 0;
+  }
+
+  MathExtra::sub3(p1,p3,edge);
+  MathExtra::sub3(pt,p3,pvec);
+  MathExtra::cross3(edge,pvec,xproduct);
+  dot = MathExtra::dot3(xproduct,norm);
+  if (dot <= 0.0) {
+    o31flag = 1;
+    if (dot == 0.0) e31flag = 1;
+    else inside = 0;
+  }
+
+  // projected point is inside tri = interior or boundary
+  // set ptflag = 1 for interior
+  // set ptflag = -1,-2,-3 for 3 edges E12,E23,E31
+  // set ptflag = -4,-5,-6 for 3 corner pts P1,P2,P3
+
+  int flag = 0;
+  if (inside) {
+    flag = 1;
+    esum = e12flag + e23flag + e31flag;
+    if (esum) {
+      if (esum == 1) {
+        if (e12flag) flag = -1;
+        else if (e23flag) flag = -2;
+        else flag = -3;
+      } else {
+        if (!e12flag) flag = -6;
+        else if (!e23flag) flag = -4;
+        else flag = -5;
+      }
+    }
+
+  // projected point is outside tri
+  // reset pt to nearest point to tri center
+  // set ptflag = -1,-2,-3 if pt on edges
+  // set ptflag = -4,-5,-6 if pt = corner pts
+
+  } else {
+    osum = o12flag + o23flag + o31flag;
+    if (osum == 1) {
+      if (o12flag) {
+        lineflag = SurfExtra::nearest_point_line(xsphere,p1,p2,pt);
+        if (lineflag == 1) flag = -1;
+        else if (lineflag == -1) flag = -4;
+        else flag = -5;
+      } else if (o23flag) {
+        lineflag = SurfExtra::nearest_point_line(xsphere,p2,p3,pt);
+        if (lineflag == 1) flag = -2;
+        else if (lineflag == -1) flag = -5;
+        else flag = -6;
+      } else {
+        lineflag = SurfExtra::nearest_point_line(xsphere,p3,p1,pt);
+        if (lineflag == 1) flag = -3;
+        else if (lineflag == -1) flag = -6;
+        else flag = -4;
+      }
+    } else {
+      if (!o12flag) {
+        flag = -6;
+        pt[0] = p3[0];
+        pt[1] = p3[1];
+        pt[2] = p3[2];
+      } else if (!o23flag) {
+        flag = -4;
+        pt[0] = p1[0];
+        pt[1] = p1[1];
+        pt[2] = p1[2];
+      } else {
+        flag = -5;
+        pt[0] = p2[0];
+        pt[1] = p2[1];
+        pt[2] = p2[2];
+      }
+    }
+  }
+
+  // test if point is exactly a corner pt
+  // if so, reset ptwhich to corner pt
+
+  /*
+  if (pt[0] == p1[0] && pt[1] == p1[1] && pt[2] == p1[2]) flag == -4;
+  else if (pt[0] == p2[0] && pt[1] == p2[1] && pt[2] == p2[2]) flag == -5;
+  else if (pt[0] == p3[0] && pt[1] == p3[1] && pt[2] == p3[2]) flag == -6;
+  */
+
+  // R = vector from nearest pt on line to Xsphere center
+  // return flag if len(R) < sphere radius
+  // else no contact, return 0
+
+  double radsq = radius * radius;
+  MathExtra::sub3(xsphere,pt,r);
+  rsq = MathExtra::lensq3(r);
+
+  if (rsq < radsq) return flag;
+  return 0;
+}
+
+/* ----------------------------------------------------------------------
+   compute nearest point between point X and line segment P1 to P2
+   return pt = nearest point within line segment
+   return 1 if pt is interior to line segment
+   return -1/-2 if pt = line segment end point 1/2
+   based on geometry.cpp::distsq_point_line() in SPARTA
+------------------------------------------------------------------------- */
+
+int nearest_point_line(double *x, double *p1, double *p2, double *pt)
+{
+  double a[3],b[3];
+
+  // A = vector from P1 to X
+  // B = vector from P1 to P2
+
+  MathExtra::sub3(x,p1,a);
+  MathExtra::sub3(p2,p1,b);
+
+  // alpha = fraction of distance from P1 to P2 that P is located at
+  // P = projected point on infinite line that is nearest to X
+  // alpha can be any value
+
+  double alpha = MathExtra::dot3(a,b) / MathExtra::lensq3(b);
+
+  // pt = point on line segment that is nearest to X
+  // if alpha <= 0.0, pt = P1, ptflag = -1
+  // if alpha >= 1.0, pt = P2, ptflag = -2
+  // else pt = P1 + alpha*(P2-P1), ptflag = 1
+
+  int ptflag;
+  if (alpha <= 0.0) {
+    ptflag = -1;
+    pt[0] = p1[0];
+    pt[1] = p1[1];
+    pt[2] = p1[2];
+  } else if (alpha >= 1.0) {
+    ptflag = -2;
+    pt[0] = p2[0];
+    pt[1] = p2[1];
+    pt[2] = p2[2];
+  } else {
+    ptflag = 1;
+    pt[0] = p1[0] + alpha*b[0];
+    pt[1] = p1[1] + alpha*b[1];
+    pt[2] = p1[2] + alpha*b[2];
+  }
+
+  return ptflag;
+}
+
+/* ---------------------------------------------------------------------- */
+
+}

src/GRANSURF/surf_extra.h

@@ -0,0 +1,28 @@
+/* -*- 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_SURF_EXTRA_H
+#define LMP_SURF_EXTRA_H
+
+namespace SurfExtra {
+
+  int overlap_sphere_line(double *, double, double *, double *,
+                          double *, double *, double &);
+  int overlap_sphere_tri(double *, double,
+                         double *, double *, double *, double *,
+                         double *, double *, double &);
+  int nearest_point_line(double *, double *, double *, double *);
+
+}
+
+#endif

src/GRANULAR/fix_wall_gran.cpp

@@ -317,9 +317,9 @@ void FixWallGran::init()
 
   if (heat_flag) {
     if (!atom->temperature_flag)
-      error->all(FLERR,"Heat conduction in fix wall/gran requires atom style with temperature property");
+      error->all(FLERR, "Heat conduction in fix wall/gran requires atom style with temperature property");
     if (!atom->heatflow_flag)
-      error->all(FLERR,"Heat conduction in fix wall/gran requires atom style with heatflow property");
+      error->all(FLERR, "Heat conduction in fix wall/gran requires atom style with heatflow property");
   }
 
   // check for FixRigid so can extract rigid body masses

src/GRANULAR/granular_model.cpp

@@ -383,7 +383,10 @@ bool GranularModel::check_contact()
     radsum = radi;
     if (radj == 0) Reff = radi;
     else Reff = radi * radj / (radi + radj);
-  } else {
+  } else if (contact_type == SURFACE) {
+    // Used by GRANSURF package
+    //   initial definitions of rsq and radj for contact
+    //   detection distinct from those in calculate_forces()
     sub3(xi, xj, dx);
     rsq = lensq3(dx);
     radsum = radi + radj;
@@ -391,6 +394,7 @@ bool GranularModel::check_contact()
   }
 
   touch = normal_model->touch();
+
   return touch;
 }
 
@@ -400,7 +404,13 @@ void GranularModel::calculate_forces()
 {
   // Standard geometric quantities
 
+  if (contact_type == SURFACE) {
+    radsum = radi;
+    Reff = radi;
+  }
+
   if (contact_type != WALLREGION) r = sqrt(rsq);
+
   rinv = 1.0 / r;
   delta = radsum - r;
   dR = delta * Reff;

src/GRANULAR/granular_model.h

@@ -32,7 +32,8 @@ enum SubModelType {
 enum ContactType {
   PAIR = 0,
   WALL = 1,
-  WALLREGION = 2
+  WALLREGION = 2,
+  SURFACE = 3
 };
 
 // forward declarations

src/GRANULAR/pair_granular.cpp

@@ -76,8 +76,11 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
   // create dummy fix as placeholder for FixNeighHistory
   // this is so final order of Modify:fix will conform to input script
 
+id_dummy = utils::strdup(std::string("NEIGH_HISTORY_GRANULAR_DUMMY") + std::to_string(instance_me));
+id_history = utils::strdup(std::string("NEIGH_HISTORY_GRANULAR") + std::to_string(instance_me));
+
   fix_history = nullptr;
-  fix_dummy = dynamic_cast<FixDummy *>(modify->add_fix("NEIGH_HISTORY_GRANULAR_DUMMY all DUMMY"));
+  fix_dummy = dynamic_cast<FixDummy *>(modify->add_fix(fmt::format("{} all DUMMY", id_dummy)));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -86,8 +89,10 @@ PairGranular::~PairGranular()
 {
   delete[] svector;
 
-  if (!fix_history) modify->delete_fix("NEIGH_HISTORY_GRANULAR_DUMMY");
-  else modify->delete_fix("NEIGH_HISTORY_GRANULAR");
+  if (!fix_history) modify->delete_fix(id_dummy);
+  else modify->delete_fix(id_history);
+  delete[] id_dummy;
+  delete[] id_history;
 
   if (allocated) {
     memory->destroy(setflag);
@@ -458,13 +463,10 @@ void PairGranular::init_style()
   // this is so its order in the fix list is preserved
 
   if (use_history && fix_history == nullptr) {
-    fix_history = dynamic_cast<FixNeighHistory *>(modify->replace_fix("NEIGH_HISTORY_GRANULAR_DUMMY",
-                                                          "NEIGH_HISTORY_GRANULAR"
-                                                          " all NEIGH_HISTORY "
-                                                          + std::to_string(size_history),1));
+    fix_history = dynamic_cast<FixNeighHistory *>(modify->replace_fix(id_dummy, fmt::format("{} all NEIGH_HISTORY {}", id_history, size_history),1));
     fix_history->pair = this;
   } else if (use_history) {
-    fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id("NEIGH_HISTORY_GRANULAR"));
+    fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id(id_history));
     if (!fix_history) error->all(FLERR,"Could not find pair fix neigh history ID");
   }
 

src/GRANULAR/pair_granular.h

@@ -58,6 +58,8 @@ class PairGranular : public Pair {
 
   class FixDummy *fix_dummy;
   class FixNeighHistory *fix_history;
+  char *id_dummy;
+  char *id_history;
 
   // storage of rigid body masses for use in granular interactions
 
@@ -69,7 +71,6 @@ class PairGranular : public Pair {
   void transfer_history(double *, double *, int, int) override;
   void prune_models();
 
- private:
   int size_history;
   int heat_flag;
 

src/Makefile

@@ -83,6 +83,7 @@ PACKAGE = \
 	fep \
 	gpu \
 	granular \
+	gransurf \
 	h5md \
 	intel \
 	interlayer \
@@ -178,6 +179,7 @@ PACKMOST = \
 	extra-pair \
 	fep \
 	granular \
+	gransurf \
 	interlayer \
 	manybody \
 	mc \

src/atom_vec_tri.cpp

@@ -61,7 +61,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
   fields_comm_vel = {"omega", "angmom"};
   fields_reverse = {"torque"};
   fields_border = {"molecule", "radius", "rmass"};
-  fields_border_vel = {"molecule", "radius", "rmass", "omega"};
+  fields_border_vel = {"molecule", "radius", "rmass", "omega", "angmom"};
   fields_exchange = {"molecule", "radius", "rmass", "omega", "angmom"};
   fields_restart = {"molecule", "radius", "rmass", "omega", "angmom"};
   fields_create = {"molecule", "radius", "rmass", "omega", "angmom", "tri"};

src/fix_move.cpp

@@ -715,8 +715,8 @@ void FixMove::initial_integrate(int /*vflag*/)
           if (omega_flag) {
             flag = 0;
             if (radius_flag && radius[i] > 0.0) flag = 1;
-            if (line_flag && line[i] >= 0.0) flag = 1;
-            if (tri_flag && tri[i] >= 0.0) flag = 1;
+            if (line_flag && line[i] >= 0) flag = 1;
+            if (tri_flag && tri[i] >= 0) flag = 1;
             if (flag) {
               omega[i][0] = omega_rotate * runit[0];
               omega[i][1] = omega_rotate * runit[1];
@@ -756,7 +756,7 @@ void FixMove::initial_integrate(int /*vflag*/)
 
           // theta for lines
 
-          if (theta_flag && line[i] >= 0.0) {
+          if (theta_flag && line[i] >= 0) {
             theta_new = fmod(toriginal[i] + arg, MY_2PI);
             avec_line->bonus[atom->line[i]].theta = theta_new;
           }
@@ -848,8 +848,8 @@ void FixMove::initial_integrate(int /*vflag*/)
           if (omega_flag) {
             flag = 0;
             if (radius_flag && radius[i] > 0.0) flag = 1;
-            if (line_flag && line[i] >= 0.0) flag = 1;
-            if (tri_flag && tri[i] >= 0.0) flag = 1;
+            if (line_flag && line[i] >= 0) flag = 1;
+            if (tri_flag && tri[i] >= 0) flag = 1;
             if (flag) {
               omega[i][0] = omega_rotate * runit[0];
               omega[i][1] = omega_rotate * runit[1];
@@ -889,7 +889,7 @@ void FixMove::initial_integrate(int /*vflag*/)
 
           // theta for lines
 
-          if (theta_flag && line[i] >= 0.0) {
+          if (theta_flag && line[i] >= 0) {
             theta_new = fmod(toriginal[i] + arg, MY_2PI);
             avec_line->bonus[atom->line[i]].theta = theta_new;
           }
@@ -1352,7 +1352,7 @@ void FixMove::set_arrays(int i)
 
       // theta for lines
 
-      if (theta_flag && line[i] >= 0.0) {
+      if (theta_flag && line[i] >= 0) {
         theta = avec_line->bonus[atom->line[i]].theta;
         toriginal[i] = theta - 0.0;    // NOTE: edit this line
       }
@@ -1415,7 +1415,7 @@ void FixMove::set_arrays(int i)
 
       // theta for lines
 
-      if (theta_flag && line[i] >= 0.0) {
+      if (theta_flag && line[i] >= 0) {
         theta = avec_line->bonus[atom->line[i]].theta;
         toriginal[i] = theta - 0.0;    // NOTE: edit this line
       }

src/fix_neigh_history.cpp

@@ -16,6 +16,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
+#include "fix_surface_global.h"
 #include "force.h"
 #include "memory.h"
 #include "modify.h"
@@ -35,7 +36,7 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), pair(nullptr), npartner(nullptr), partner(nullptr), valuepartner(nullptr),
     ipage_atom(nullptr), dpage_atom(nullptr), ipage_neigh(nullptr), dpage_neigh(nullptr)
 {
-  if (narg != 4) error->all(FLERR, "Illegal fix NEIGH_HISTORY command");
+  if (narg < 4) error->all(FLERR, "Illegal fix NEIGH_HISTORY command");
 
   restart_peratom = 1;
   restart_global = 1;
@@ -53,8 +54,17 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
   for (int i = 0; i < dnum; i++) zeroes[i] = 0.0;
 
   onesided = 0;
-  if (strcmp(id, "LINE_NEIGH_HISTORY") == 0) onesided = 1;
-  if (strcmp(id, "TRI_NEIGH_HISTORY") == 0) onesided = 1;
+  surface_global = 0;
+  int iarg = 4;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "onesided") == 0) onesided = 1;
+    else if (strcmp(arg[iarg], "surface/global") == 0) surface_global = 1;
+    else error->all(FLERR, "Illegal fix neigh/history command {}", arg[iarg]);
+    iarg += 1;
+  }
+
+  if (surface_global && !onesided)
+    error->all(FLERR, "Surface global must be used with onesided");
 
   if (newton_pair)
     comm_reverse = 1;    // just for single npartner value
@@ -262,7 +272,11 @@ void FixNeighHistory::pre_exchange_onesided()
   for (i = 0; i < nlocal_neigh; i++) npartner[i] = 0;
 
   tagint *tag = atom->tag;
-  NeighList *list = pair->list;
+  NeighList *list;
+  if (surface_global)
+    list = fix->list;
+  else
+    list = pair->list;
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;
@@ -308,6 +322,9 @@ void FixNeighHistory::pre_exchange_onesided()
         j = jlist[jj];
         j &= NEIGHMASK;
         m = npartner[i]++;
+        if (surface_global)
+          partner[i][m] = j;
+        else
           partner[i][m] = tag[j];
         memcpy(&valuepartner[i][dnum * m], onevalues, dnumbytes);
       }
@@ -616,7 +633,11 @@ void FixNeighHistory::post_neighbor()
   dpage_neigh->reset();
 
   tagint *tag = atom->tag;
-  NeighList *list = pair->list;
+  NeighList *list;
+  if (surface_global)
+    list = fix->list;
+  else
+    list = pair->list;
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;
@@ -634,7 +655,7 @@ void FixNeighHistory::post_neighbor()
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
 
-      if (use_bit_flag) {
+      if (use_bit_flag && !surface_global) {
         rflag = histmask(j) | pair->beyond_contact;
         j &= HISTMASK;
         jlist[jj] = j;
@@ -652,9 +673,14 @@ void FixNeighHistory::post_neighbor()
       // apply a mask for history (and they could use the bits for special bonds)
 
       if (rflag) {
+        if (surface_global) {
+          for (m = 0; m < np; m++)
+            if (partner[i][m] == j) break;
+        } else {
           jtag = tag[j];
           for (m = 0; m < np; m++)
             if (partner[i][m] == jtag) break;
+        }
         if (m < np) {
           allflags[jj] = 1;
           memcpy(&allvalues[nn], &valuepartner[i][dnum * m], dnumbytes);

src/fix_neigh_history.h

@@ -29,9 +29,10 @@ class FixNeighHistory : public Fix {
   int nlocal_neigh;            // nlocal at last time neigh list was built
   int nall_neigh;              // ditto for nlocal+nghost
   int use_bit_flag;            // flag whether this fix uses the extra bit in the nlist
-  int **firstflag;        // ptr to each atom's neighbor flsg
+  int **firstflag;             // ptr to each atom's neighbor flag
   double **firstvalue;         // ptr to each atom's values
   class Pair *pair;            // ptr to pair style that uses neighbor history
+  class FixSurfaceGlobal *fix; // ptr to fix surface/global that uses neighbor history
 
   FixNeighHistory(class LAMMPS *, int, char **);
   ~FixNeighHistory() override;
@@ -62,11 +63,17 @@ class FixNeighHistory : public Fix {
 
   int get_dnum() const { return dnum; }
   int get_maxpartner() const { return maxpartner; }
+  int *get_npartner() const { return npartner; }
+  tagint **get_partner() const { return partner; }
+  double **get_valuepartner() const { return valuepartner; }
+  MyPage<tagint> *get_ipage_atom() const { return ipage_atom; }
+  MyPage<double> *get_dpage_atom() const { return dpage_atom; }
 
  protected:
   int newton_pair;        // same as force setting
   int dnum, dnumbytes;    // dnum = # of values per neighbor
   int onesided;           // 1 for line/tri history, else 0
+  int surface_global;     // 1 for surface/global, else 0
 
   int maxatom;     // max size of firstflag and firstvalue
   int commflag;    // mode of reverse comm to get ghost info

src/memory.h

@@ -242,6 +242,10 @@ class Memory : protected Pointers {
     return array;
   }
 
+/* ----------------------------------------------------------------------
+   create a 3d array with a ragged 3rd dimension
+------------------------------------------------------------------------- */
+
   template <typename TYPE>
   TYPE ***create_ragged(TYPE ***&array, int n1, int *n2, int **n3, const char *name)
   {

src/molecule.cpp

@@ -41,7 +41,10 @@ static constexpr double SINERTIA = 0.4;    // moment of inertia prefactor for sp
 
 Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
     Pointers(lmp), id(nullptr), x(nullptr), type(nullptr), molecule(nullptr), q(nullptr),
-    radius(nullptr), rmass(nullptr), mu(nullptr), num_bond(nullptr), bond_type(nullptr),
+    radius(nullptr), rmass(nullptr), mu(nullptr),
+    lines(nullptr), tris(nullptr),
+    molline(nullptr), typeline(nullptr), moltri(nullptr), typetri(nullptr),
+    num_bond(nullptr), bond_type(nullptr),
     bond_atom(nullptr), num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr),
     angle_atom2(nullptr), angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr),
     dihedral_atom1(nullptr), dihedral_atom2(nullptr), dihedral_atom3(nullptr),
@@ -155,7 +158,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
   // stats
 
   if (title.empty()) title = "(no title)";
-  if (me == 0)
+  if (me == 0) {
     utils::logmesg(lmp,
                    "Read molecule template {}:\n{}\n"
                    "  {} molecules\n"
@@ -167,6 +170,9 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
                    "  {} impropers with max type {}\n",
                    id, title, nmolecules, nfragments, natoms, ntypes, nbonds, nbondtypes, nangles,
                    nangletypes, ndihedrals, ndihedraltypes, nimpropers, nimpropertypes);
+    if (nlines) utils::logmesg(lmp,"  {} lines\n",nlines);
+    if (ntris) utils::logmesg(lmp,"  {} triangles\n",ntris);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -442,6 +448,7 @@ void Molecule::read(int flag)
     if (text.empty()) continue;
 
     // search line for header keywords and set corresponding variable
+
     try {
       ValueTokenizer values(text);
 
@@ -450,6 +457,14 @@ void Molecule::read(int flag)
       if (values.matches("^\\s*\\d+\\s+atoms")) {
         natoms = values.next_int();
         nwant = 2;
+
+      } else if (values.matches("^\\s*\\d+\\s+lines")) {
+        nlines = values.next_int();
+        nwant = 2;
+      } else if (values.matches("^\\s*\\d+\\s+triangles")) {
+        ntris = values.next_int();
+        nwant = 2;
+
       } else if (values.matches("^\\s*\\d+\\s+bonds")) {
         nbonds = values.next_int();
         nwant = 2;
@@ -462,6 +477,7 @@ void Molecule::read(int flag)
       } else if (values.matches("^\\s*\\d+\\s+impropers")) {
         nimpropers = values.next_int();
         nwant = 2;
+
       } else if (values.matches("^\\s*\\d+\\s+fragments")) {
         nfragments = values.next_int();
         nwant = 2;
@@ -519,15 +535,31 @@ void Molecule::read(int flag)
 
   // error checks
 
-  if (natoms < 1) error->all(FLERR, "No atoms or invalid atom count in molecule file");
+  if (natoms < 0) error->all(FLERR, "No atoms or invalid atom count in molecule file");
+  if (nlines < 0) error->all(FLERR,"Invalid line count in molecule file");
+  if (ntris < 0) error->all(FLERR,"Invalid triangle count in molecule file");
+
   if (nbonds < 0) error->all(FLERR, "Invalid bond count in molecule file");
   if (nangles < 0) error->all(FLERR, "Invalid angle count in molecule file");
   if (ndihedrals < 0) error->all(FLERR, "Invalid dihedral count in molecule file");
   if (nimpropers < 0) error->all(FLERR, "Invalid improper count in molecule file");
 
-  // count = vector for tallying bonds,angles,etc per atom
+  if (natoms == 0 && nlines == 0 && ntris == 0)
+    error->all(FLERR,"Molecule file must define either atoms or lines or triangles");
 
-  if (flag == 0) memory->create(count, natoms, "molecule:count");
+  if (nlines && domain->dimension != 2)
+    error->all(FLERR,"Molecule file with lines must be for 2d simulation");
+  if (ntris && domain->dimension != 3)
+    error->all(FLERR,"Molecule file with triangles must be for 3d simulation");
+
+  // count = vector for tallying values in different sections of file
+  // set length to max of natoms, nlines, ntris
+
+  if (flag == 0) {
+    int maxcount = MAX(natoms,nlines);
+    maxcount = MAX(maxcount,ntris);
+    memory->create(count, maxcount, "molecule:count");
+  }
 
   // grab keyword and skip next line
 
@@ -588,6 +620,19 @@ void Molecule::read(int flag)
       else
         skip_lines(natoms, line, keyword);
 
+    } else if (keyword == "Lines") {
+      lineflag = 1;
+      if (flag)
+        line_segments(line);
+      else
+        skip_lines(nlines, line, keyword);
+    } else if (keyword == "Triangles") {
+      triflag = 1;
+      if (flag)
+        triangles(line);
+      else
+        skip_lines(ntris, line, keyword);
+
     } else if (keyword == "Bonds") {
       if (nbonds == 0) error->all(FLERR, "Found Bonds section but no nbonds setting in header");
       bondflag = tag_require = 1;
@@ -819,8 +864,8 @@ void Molecule::types(char *line)
 }
 // clang-format off
 /* ----------------------------------------------------------------------
-   read molecules from file
-   set nmolecules = max of any molecule type
+   read molecule IDs from file
+   set nmolecules = max of any molecule ID
 ------------------------------------------------------------------------- */
 
 void Molecule::molecules(char *line)
@@ -1025,6 +1070,124 @@ void Molecule::masses(char *line)
   }
 }
 
+/* ----------------------------------------------------------------------
+   read line segments from file
+   do NOT subtract one from point indices
+------------------------------------------------------------------------- */
+
+void Molecule::line_segments(char *line)
+{
+  for (int i = 0; i < nlines; i++) count[i] = 0;
+  try {
+    for (int i = 0; i < nlines; i++) {
+      readline(line);
+
+      ValueTokenizer values(utils::trim_comment(line));
+      if (values.count() != 7)
+        error->all(FLERR, "Invalid line in Lines section of molecule file: {}", line);
+
+      int iline = values.next_int() - 1;
+      if (iline < 0 || iline >= nlines)
+        error->all(FLERR, "Invalid line index in Lines section of molecule file");
+      count[iline]++;
+      molline[iline] = values.next_int();
+      typeline[iline] = values.next_int();
+      lines[iline][0] = values.next_double();
+      lines[iline][1] = values.next_double();
+      lines[iline][2] = values.next_double();
+      lines[iline][3] = values.next_double();
+
+      // apply geometric operations to line points
+
+      lines[iline][0] *= sizescale;
+      lines[iline][1] *= sizescale;
+      lines[iline][2] *= sizescale;
+      lines[iline][3] *= sizescale;
+    }
+  } catch (TokenizerException &e) {
+    error->all(FLERR, "Invalid line in Lines section of molecule file: {}\n{}", e.what(), line);
+  }
+
+  // check all line molecule-IDs and types
+  // add toffset to line type
+
+  for (int i = 0; i < nlines; i++) {
+    if (count[i] == 0)
+      error->all(FLERR, "Line {} missing in Lines section of molecule file", i + 1);
+    if (molline[i] < 0)
+      error->all(FLERR,"Invalid line molecule ID in molecule file");
+    if (typeline[i] <= 0)
+      error->all(FLERR,"Invalid line type in molecule file");
+
+    typeline[i] += toffset;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   read triangles from file
+   do NOT subtract one from point indices
+------------------------------------------------------------------------- */
+
+void Molecule::triangles(char *line)
+{
+  for (int i = 0; i < ntris; i++) count[i] = 0;
+  try {
+    for (int i = 0; i < ntris; i++) {
+      readline(line);
+
+      ValueTokenizer values(utils::trim_comment(line));
+      if (values.count() != 12)
+        error->all(FLERR, "Invalid triangle in Triangles section of molecule file: {}", line);
+
+      int itri = values.next_int() - 1;
+      if (itri < 0 || itri >= ntris)
+        error->all(FLERR, "Invalid triangle index in Triangles section of molecule file");
+      count[itri]++;
+      moltri[itri] = values.next_int();
+      typetri[itri] = values.next_int();
+
+      tris[itri][0] = values.next_double();
+      tris[itri][1] = values.next_double();
+      tris[itri][2] = values.next_double();
+      tris[itri][3] = values.next_double();
+      tris[itri][4] = values.next_double();
+      tris[itri][5] = values.next_double();
+      tris[itri][6] = values.next_double();
+      tris[itri][7] = values.next_double();
+      tris[itri][8] = values.next_double();
+
+      // apply geometric operations to triangle points
+
+      tris[itri][0] *= sizescale;
+      tris[itri][1] *= sizescale;
+      tris[itri][2] *= sizescale;
+      tris[itri][3] *= sizescale;
+      tris[itri][4] *= sizescale;
+      tris[itri][5] *= sizescale;
+      tris[itri][6] *= sizescale;
+      tris[itri][7] *= sizescale;
+      tris[itri][8] *= sizescale;
+    }
+
+  } catch (TokenizerException &e) {
+    error->all(FLERR, "Invalid tri in Triangles section of molecule file: {}\n{}", e.what(), line);
+  }
+
+  // check all triangle molecule-IDs and types
+  // add toffset to triangle type
+
+  for (int i = 0; i < ntris; i++) {
+    if (count[i] == 0)
+      error->all(FLERR, "Triangle {} missing in Triangles section of molecule file", i + 1);
+    if (moltri[i] < 0)
+      error->all(FLERR,"Invalid triangle molecule ID in molecule file");
+    if (typetri[i] <= 0)
+      error->all(FLERR,"Invalid triangle type in molecule file");
+
+    typetri[i] += toffset;
+  }
+}
+
 /* ----------------------------------------------------------------------
    read bonds from file
    set nbondtypes = max type of any bond
@@ -1921,6 +2084,7 @@ void Molecule::initialize()
   nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
   nibody = ndbody = 0;
   nfragments = 0;
+  nlines = ntris = 0;
 
   bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
   maxspecial = 0;
@@ -1930,6 +2094,7 @@ void Molecule::initialize()
   nspecialflag = specialflag = 0;
   shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
   bodyflag = ibodyflag = dbodyflag = 0;
+  lineflag = triflag = 0;
 
   centerflag = massflag = comflag = inertiaflag = 0;
   tag_require = 0;
@@ -1940,6 +2105,13 @@ void Molecule::initialize()
   radius = nullptr;
   rmass = nullptr;
 
+  molline = NULL;
+  typeline = NULL;
+  lines = NULL;
+  moltri = NULL;
+  typetri = NULL;
+  tris = NULL;
+
   num_bond = nullptr;
   bond_type = nullptr;
   bond_atom = nullptr;
@@ -1992,6 +2164,19 @@ void Molecule::allocate()
   if (radiusflag) memory->create(radius, natoms, "molecule:radius");
   if (rmassflag) memory->create(rmass, natoms, "molecule:rmass");
 
+  // lines or triangles with corner points
+
+  if (lineflag) {
+    memory->create(molline,nlines,"molecule:molline");
+    memory->create(typeline,nlines,"molecule:typeline");
+    memory->create(lines,nlines,4,"molecule:lines");
+  }
+  if (triflag) {
+    memory->create(moltri,ntris,"molecule:moltri");
+    memory->create(typetri,ntris,"molecule:typetri");
+    memory->create(tris,ntris,9,"molecule:tris");
+  }
+
   // always allocate num_bond,num_angle,etc and nspecial
   // even if not in molecule file, initialize to 0
   // this is so methods that use these arrays don't have to check they exist
@@ -2068,6 +2253,13 @@ void Molecule::deallocate()
 
   if (fragmentflag) { fragmentnames.clear(); }
 
+  memory->destroy(molline);
+  memory->destroy(typeline);
+  memory->destroy(lines);
+  memory->destroy(moltri);
+  memory->destroy(typetri);
+  memory->destroy(tris);
+
   memory->destroy(num_bond);
   memory->destroy(bond_type);
   memory->destroy(bond_atom);

src/molecule.h

@@ -29,12 +29,14 @@ class Molecule : protected Pointers {
 
   // number of atoms,bonds,etc in molecule
   // nibody,ndbody = # of integer/double fields in body
+  // number of lines or triangles
 
   int natoms;
   int nbonds, nangles, ndihedrals, nimpropers;
   int ntypes, nmolecules, nfragments;
   int nbondtypes, nangletypes, ndihedraltypes, nimpropertypes;
   int nibody, ndbody;
+  int nlines,ntris;
 
   // max bond,angle,etc per atom
 
@@ -48,6 +50,7 @@ class Molecule : protected Pointers {
   int nspecialflag, specialflag;
   int shakeflag, shakeflagflag, shakeatomflag, shaketypeflag;
   int bodyflag, ibodyflag, dbodyflag;
+  int lineflag, triflag;
 
   // 1 if attribute defined or computed, 0 if not
 
@@ -61,12 +64,19 @@ class Molecule : protected Pointers {
 
   double **x;          // displacement of each atom from origin
   int *type;           // type of each atom
-  tagint *molecule;    // molecule of each atom
+  tagint *molecule;    // molecule-ID of each atom
   double *q;           // charge on each atom
   double *radius;      // radius of each atom
   double *rmass;       // mass of each atom
   double **mu;         // dipole vector of each atom
 
+  int *molline;        // molecule-ID of each line
+  int *typeline;       // type of each line
+  double **lines;      // line end points
+  int *moltri;         // molecule-ID of each triangles
+  int *typetri;        // type of each triangle
+  double **tris;       // triangle corner points
+
   int *num_bond;    // bonds, angles, dihedrals, impropers for each atom
   int **bond_type;
   tagint **bond_atom;
@@ -147,6 +157,8 @@ class Molecule : protected Pointers {
   void diameters(char *);
   void dipoles(char *);
   void masses(char *);
+  void line_segments(char *);
+  void triangles(char *);
   void bonds(int, char *);
   void angles(int, char *);
   void dihedrals(int, char *);

src/my_pool_chunk.cpp

@@ -85,6 +85,7 @@ MyPoolChunk<T>::MyPoolChunk(int user_minchunk, int user_maxchunk, int user_nbin,
 }
 
 /** Destroy class instance and free all allocated memory */
+
 template <class T> MyPoolChunk<T>::~MyPoolChunk()
 {
   delete[] freehead;

src/neigh_request.cpp

@@ -277,6 +277,7 @@ void NeighRequest::apply_flags(int flags)
   if (flags & REQ_RESPA_INOUT) { respainner = respaouter = 1; }
   if (flags & REQ_RESPA_ALL)   { respainner = respamiddle = respaouter = 1; }
   if (flags & REQ_SSA)         { ssa = 1; }
+  if (flags & REQ_ONESIDED)    { granonesided = 1; }
   // clang-format on
 }
 

src/neighbor.cpp

@@ -946,8 +946,8 @@ int Neighbor::init_pair()
 
     flag = choose_pair(requests[i]);
     lists[i]->pair_method = flag;
-    if (flag < 0)
-      error->all(FLERR,"Requested neighbor pair method does not exist");
+    if (flag < 0 && comm->me == 0)
+      error->warning(FLERR,"Requested neighbor pair method does not exist");
   }
 
   // instantiate unique Bin,Stencil classes in neigh_bin & neigh_stencil vecs
@@ -1283,11 +1283,12 @@ void Neighbor::morph_skip()
       // these flags must be same,
       //   else 2 lists do not store same pairs
       //   or their data structures are different
-      // NOTE: need check for 2 Kokkos flags?
+      // no need to check for history flag
+      //   it does not affect what pairs are stored in neigh list
+      // NOTE: need to check for 2 Kokkos flags ?
 
       if (irq->ghost != jrq->ghost) continue;
       if (irq->size != jrq->size) continue;
-      if (irq->history != jrq->history) continue;
       if (irq->bond != jrq->bond) continue;
       if (irq->omp != jrq->omp) continue;
       if (irq->intel != jrq->intel) continue;
@@ -1304,12 +1305,12 @@ void Neighbor::morph_skip()
     // else create a new identical list except non-skip
     // for new list, set neigh = 1, skip = 0, no skip vec/array,
     //   copy unique flag (since copy_request() will not do it)
-    // note: parents of skip lists do not have associated history
-    //   b/c child skip lists have the associated history
+    // ensure parent history flag is set if any child sets history flag
 
     if (jj < nrequest) {
       irq->skiplist = j;
       irq->trim = trim_flag;
+      if (irq->history) jrq->history = 1;
     } else {
       int newrequest = request(this,-1);
       irq->skiplist = newrequest;
@@ -1319,6 +1320,7 @@ void Neighbor::morph_skip()
       nrq->pair = nrq->fix = nrq->compute = nrq->command = 0;
       nrq->neigh = 1;
       nrq->skip = 0;
+      if (irq->history) nrq->history = 1;
       if (irq->unique) nrq->unique = 1;
 
       sort_requests();
@@ -1374,8 +1376,8 @@ void Neighbor::morph_granular()
     // force parent newton off (newton = 2) to enable onesided skip by child
     // set parent granonesided = 0, so it stores all neighs in usual manner
     // set off2on = 1 for all children, since they expect newton on lists
-    //   this is b/c granonesided only set by line/gran and tri/gran which
-    //   both require system newton on
+    //   this is b/c granonesided is currently only set by line/tri gran
+    //   both of those pair styles require newton on
 
     if (onesided == 2) {
       irq->newton = 2;
@@ -1447,10 +1449,12 @@ void Neighbor::morph_halffull()
       // these flags must be same,
       //   else 2 lists do not store same pairs
       //   or their data structures are different
+      // no need to check for history flag
+      //   it does not affect what pairs are stored in neigh list
+      // NOTE: need to check for 2 Kokkos flags ?
 
       if (irq->ghost != jrq->ghost) continue;
       if (irq->size != jrq->size) continue;
-      if (irq->history != jrq->history) continue;
       if (irq->bond != jrq->bond) continue;
       if (irq->omp != jrq->omp) continue;
       if (irq->intel != jrq->intel) continue;
@@ -1556,11 +1560,13 @@ void Neighbor::morph_copy_trim()
       // these flags must be same,
       //   else 2 lists do not store same pairs
       //   or their data structures are different
-      // no need to check omp b/c it stores same pairs
-      // NOTE: need check for 2 Kokkos flags?
+      // ghost flag logic was checked above
+      // no need to check for history flag
+      //   it does not affect what pairs are stored in neigh list
+      // no need to check for omp flag b/c it stores same pairs
+      // NOTE: need to check for 2 Kokkos flags ?
 
       if (irq->size != jrq->size) continue;
-      if (irq->history != jrq->history) continue;
       if (irq->bond != jrq->bond) continue;
       if (irq->intel != jrq->intel) continue;
       if (irq->kokkos_host && !jrq->kokkos_host) continue;
@@ -2104,11 +2110,11 @@ int Neighbor::choose_pair(NeighRequest *rq)
 
   int molecular = atom->molecular;
 
-  //printf("PAIR RQ FLAGS: hf %d %d n %d g %d sz %d gos %d r %d b %d o %d i %d "
-  //       "kk %d %d ss %d dn %d sk %d cp %d hf %d oo %d\n",
+  //printf("PAIR RQ FLAGS: hf %d %d nw %d gh %d sz %d gos %d ro %d bn %d om %d in %d "
+  //       "kk %d %d ss %d sk %d cp %d hf %d o2o %d\n",
   //       rq->half,rq->full,rq->newton,rq->ghost,rq->size,
   //       rq->granonesided,rq->respaouter,rq->bond,rq->omp,rq->intel,
-  //       rq->kokkos_host,rq->kokkos_device,rq->ssa,rq->dnum,
+  //       rq->kokkos_host,rq->kokkos_device,rq->ssa,
   //       rq->skip,rq->copy,rq->halffull,rq->off2on);
 
   // use request and system settings to match exactly one NPair class mask

src/neighbor.h

@@ -355,6 +355,7 @@ namespace NeighConst {
     REQ_NEWTON_ON = 1 << 8,
     REQ_NEWTON_OFF = 1 << 9,
     REQ_SSA = 1 << 10,
+    REQ_ONESIDED = 1 << 11
   };
 }    // namespace NeighConst
 

src/stl_reader.cpp

@@ -0,0 +1,192 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   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 "stl_reader.h"
+
+#include "comm.h"
+#include "error.h"
+#include "memory.h"
+#include "text_file_reader.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 16384
+
+/* ---------------------------------------------------------------------- */
+
+STLReader::STLReader(LAMMPS *lmp) : Pointers(lmp)
+{
+  ntris = maxtris = 0;
+  tris = nullptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+STLReader::~STLReader()
+{
+  memory->destroy(tris);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int STLReader::read_file(const char *filename, double **&caller_tris)
+{
+  int me = comm->me;
+
+  if (me == 0) {
+
+    // open file (text or binary)
+
+    FILE *fp = fopen(filename, "rb");
+    if (fp == nullptr) error->one(FLERR, "Cannot open file {}: {}", filename, utils::getsyserror());
+
+    // try reading the file in ASCII format
+
+    TextFileReader reader(fp, "STL mesh");
+
+    try {
+
+      char *line = reader.next_line();
+      if (!line || !utils::strmatch(line, "^solid"))
+        throw TokenizerException("Invalid STL mesh file format", "");
+
+      line += 6;
+      if (utils::strmatch(line, "^binary"))
+        throw TokenizerException("Invalid STL mesh file format", "");
+
+      utils::logmesg(lmp, "Reading STL object {} from text file {}\n", utils::trim(line), filename);
+
+      while ((line = reader.next_line())) {
+
+        // next line is facet line with 5 words
+
+        auto values = utils::split_words(line);
+
+        // otherwise next line should be endsolid and are done reading file
+
+        if ((values.size() != 5) || !utils::strmatch(values[0], "^facet")) {
+          if (!utils::strmatch(values[0], "^endsolid"))
+            throw TokenizerException("Error reading endsolid", "");
+          break;
+        }
+
+        // ignore normal
+
+        line = reader.next_line(2);
+        if (!line || !utils::strmatch(line, "^ *outer *loop"))
+          throw TokenizerException("Error reading outer loop", "");
+
+        // three corner points of a single triangle
+
+        if (ntris == maxtris) {
+          maxtris += DELTA;
+          memory->grow(tris,maxtris,9,"stl_reader:tris");
+        }
+
+        for (int k = 0; k < 3; ++k) {
+          line = reader.next_line(4);
+          values = utils::split_words(line);
+          if ((values.size() != 4) || !utils::strmatch(values[0], "^vertex"))
+            throw TokenizerException("Error reading vertex", "");
+
+          tris[ntris][3*k+0] = utils::numeric(FLERR, values[1], false, lmp);
+          tris[ntris][3*k+1] = utils::numeric(FLERR, values[2], false, lmp);
+          tris[ntris][3*k+2] = utils::numeric(FLERR, values[3], false, lmp);
+        }
+
+        line = reader.next_line(1);
+        if (!line || !utils::strmatch(line, "^ *endloop"))
+          throw TokenizerException("Error reading endloop", "");
+        line = reader.next_line(1);
+        if (!line || !utils::strmatch(line, "^ *endfacet"))
+          throw TokenizerException("Error reading endfacet", "");
+
+        ntris++;
+      }
+
+    // if read as text file failed, try reading as binary file
+
+    } catch (std::exception &e) {
+
+      if (utils::strmatch(e.what(), "^Invalid STL mesh file format")) {
+        char title[80];
+        float triangle[12];
+        uint32_t untri;
+        uint16_t attr;
+        size_t count;
+
+        rewind(fp);
+        count = fread(title, sizeof(char), 80, fp);
+        title[79] = '\0';
+        count = fread(&untri, sizeof(untri), 1, fp);
+        if (count <= 0) {
+          error->one(FLERR, "Error reading STL file {}: {}", filename, utils::getsyserror());
+        } else {
+          utils::logmesg(lmp, "Reading STL object {} from binary file {}\n", utils::trim(title),
+                         filename);
+        }
+
+        if (untri > MAXSMALLINT)
+          error->one(FLERR, "Triangle counts in STL file exceed integer limit");
+
+        ntris = untri;
+        memory->create(tris,ntris,9,"stl_reader:tris");
+
+        for (int i = 0; i < ntris; ++i) {
+          count = fread(triangle, sizeof(float), 12, fp);
+          if (count != 12)
+            error->one(FLERR, "Error reading STL file {}: {}", filename, utils::getsyserror());
+          count = fread(&attr, sizeof(attr), 1, fp);
+
+          // ignore normal
+
+          int m = 0;
+          for (int j = 0; j < 3; ++j)
+            for (int k = 0; k < 3; ++k)
+              tris[i][m++] = triangle[3*j + k + 3];
+        }
+
+      } else {
+        error->all(FLERR, "Error reading STL file {}: {}", filename, e.what());
+      }
+    }
+
+    if (fp) fclose(fp);
+  }
+
+  // MPI broadcast of triangle vertex coords to all procs
+  // allow for 9*ntris to exceed max-allowed size of MPI_Bcast()
+
+  MPI_Bcast(&ntris,1,MPI_INT,0,world);
+  if (ntris == 0) error->all(FLERR,"STL file has no triangles");
+  if (me) memory->create(tris,ntris,9,"stl_reader:tris");
+
+  bigint ntotal = (bigint) ntris * 9;
+  if (ntotal < MAXSMALLINT)
+    MPI_Bcast(&tris[0][0],9*ntris,MPI_DOUBLE,0,world);
+  else {
+    double *source = &tris[0][0];
+    bigint n = 0;
+    while (n < ntotal) {
+      int nsize = MIN(MAXSMALLINT,ntotal-n);
+      MPI_Bcast(&source[n],nsize,MPI_DOUBLE,0,world);
+      n += nsize;
+    }
+  }
+
+  // return values
+
+  caller_tris = tris;
+  return ntris;
+}

src/stl_reader.h

@@ -0,0 +1,35 @@
+/* -*- 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_STL_READER_H
+#define LMP_STL_READER_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class STLReader : protected Pointers {
+ public:
+  STLReader(class LAMMPS *);
+  ~STLReader();
+  int read_file(const char *, double **&);
+
+ private:
+  int ntris,maxtris;
+  double **tris;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif

tools/README

@@ -25,6 +25,7 @@ eam_generate           2nd tool to generate EAM alloy potential files
 eff                    scripts for working with the eFF (electron force field)
 emacs                  add-ons to EMACS editor for editing LAMMPS input scripts
 fep                    scripts for free-energy perturbation with FEP pkg
+granlar_surfaces       scripts for working with surfaces of tris/lines (3d/2d)
 i-pi                   Python wrapper for performing path-integral MD (PIMD)
 ipp                    input pre-processor Perl tool for creating input scripts
 kate                   add-ons to Kate editor for editing LAMMPS input scripts

tools/gransurf/refine.py

@@ -0,0 +1,704 @@
+#!/usr/bin/env python
+
+# Script:  refine.py
+# Purpose: refine a set of granular surface elements for input to LAMMPS
+#          elements in 2d = line segments, elements in 3d = triangles
+# Syntax:  refine.py dim insource infile thresh outsource outfile
+#          dim = 2 or 3
+#          insource = mol for molecule file, stl for STL file
+#          infile = molecule or STL filename
+#          thresh = max size of resulting surface eleents
+#          outsource = mol for molecule file, stl for STL file
+#          outfile = molecule or STL filename
+# Author:  Steve Plimpton (Sandia), sjplimp at gmail.com
+
+# TODO:
+# print stats at each stage
+# could also work with local surfs via data and/or dump file
+# howto assign tri type, molID for output into molfile
+#   maybe should be persisted from input molfile (but not input STL)
+
+import sys
+from operator import itemgetter
+from math import sqrt
+
+# ----------
+# classes
+# ----------
+
+class Point:
+  def __init__(self,x,y,z):
+    self.x = (x,y,z)
+
+class Line:
+  def __init__(self,point1,point2):
+    self.active = 1
+    self.point1 = point1
+    self.point2 = point2
+    self.p1 = self.p2 = -1
+
+class Edge:                  # unique tri edges
+  def __init__(self,p1,p2):
+    self.active = 1
+    self.p1 = p1
+    self.p2 = p2
+    self.neigh = []
+    self.which = []
+  
+class Tri:
+  def __init__(self,point1,point2,point3):
+    self.active = 1
+    self.point1 = point1
+    self.point2 = point2
+    self.point3 = point3
+    self.p1 = self.p2 = self.p3 = -1
+    
+# ----------
+# functions
+# ----------
+
+def error(txt=None):
+  if not txt: print("Syntax: refine.py dim insource infile thresh outsource outfile")
+  else: print("ERROR:",txt)
+  sys.exit()
+
+def distance(x1,x2):
+  dx = x1[0] - x2[0]
+  dy = x1[1] - x2[1]
+  dz = x1[2] - x2[2]
+  r = sqrt(dx*dx + dy*dy + dz*dz)
+  return r
+
+def midpt(x1,x2):
+  xnew = 0.5 * (x1[0] + x2[0])
+  ynew = 0.5 * (x1[1] + x2[1])
+  znew = 0.5 * (x1[2] + x2[2])
+  return (xnew,ynew,znew)
+
+# mybisect in place of Python 3.10 bisect module
+# NOTE: explain why Python module does not work
+# forward: one > all values before its insertion point
+# reverse: one > all values after its insertion point
+
+def mybisect(vec,one,func,reverse):
+  value = func(one)
+  ilo = 0
+  ihi = len(vec)
+  niter = 0
+  while 1:
+    if niter > 10: break
+    niter += 1
+    imid = (ilo+ihi) // 2
+    if ilo == ihi: break
+    if not reverse:
+      if value <= func(vec[imid]): ihi = imid
+      else: ilo = imid+1
+    else:
+      if value > func(vec[imid]): ihi = imid
+      else: ilo = imid+1
+  return imid
+
+# debug functions
+
+def print_lines(txt,lines):
+  nactive = 0
+  for line in lines:
+    if line.active: nactive += 1
+  print(txt,len(lines),nactive)
+  for iline,line in enumerate(lines):
+    if not line.active: continue
+    print(iline,line.active,distance(points[line.p1].x,points[line.p2].x),
+              line.point1,line.point2)
+
+def print_edges(txt,edges):
+  nactive = 0
+  for edge in edges:
+    if edge.active: nactive += 1
+  print(txt,len(edges),nactive)
+  for iedge,edge in enumerate(edges):
+    if not edge.active: continue
+    print(iedge,edge.active,distance(points[edge.p1].x,points[edge.p2].x),
+          edge.p1,edge.p2,points[edge.p1].x,points[edge.p2].x,
+          edge.neigh,edge.which)
+
+def print_tris(txt,tris):
+  nactive = 0
+  for tri in tris:
+    if tri.active: nactive += 1
+  print(txt,len(tris),nactive)
+  for itri,tri in enumerate(tris):
+    if not tri.active: continue
+    print(itri,tri.active,distance(points[tri.p1].x,points[tri.p2].x),
+              distance(points[tri.p2].x,points[tri.p3].x),
+              distance(points[tri.p3].x,points[tri.p1].x),
+              tri.point1,tri.point2,tri.point3)
+
+# read a molecule file with lines
+
+def read_molfile_2d(filename):
+  filelines = open(filename,"r").readlines()[1:]
+
+  nlines = 0
+
+  # read header of molecule file
+  
+  for i,oneline in enumerate(filelines):
+    oneline = oneline.strip()
+    if not oneline: continue
+    if oneline[0] == '#': continue
+    if nlines: break
+    words = oneline.split()
+    if words[1] == "lines": nlines = int(words[0])
+    if nlines <= 0: error("Molecule file header is invalid for 2d lines")
+
+  # read Lines section of molecule file
+
+  section_word = 0
+  count = 0
+  lines = []
+  
+  for oneline in filelines[i:]:
+    oneline = oneline.strip()
+    if not oneline: continue
+    if section_word == 0:
+      if oneline != "Lines":
+        error("Molecule file section is invalid for 2d lines")
+      section_word = 1
+      continue
+    count += 1
+    words = oneline.split()
+    if int(words[0]) != count:
+      error("Molecule file section is invalid for 2d lines")
+    line = Line((float(words[3]),float(words[4]),0.0),
+                (float(words[5]),float(words[6]),0.0))
+    lines.append(line)
+
+  if count != nlines:
+    error("Molecule file section is invalid for 2d lines")
+    
+  return lines
+
+# read a molecule file with tris
+
+def read_molfile_3d(filename):
+  filelines = open(filename,"r").readlines()[1:]
+
+  ntris = 0
+
+  # read header of molecule file
+  
+  for i,oneline in enumerate(filelines):
+    oneline = oneline.strip()
+    if not oneline: continue
+    if oneline[0] == '#': continue
+    if ntris: break
+    words = oneline.split()
+    if words[1] == "triangles": ntris = int(words[0])
+    if ntris <= 0: error("Molecule file header is invalid for 3d triangles")
+
+  # read Lines section of molecule file
+
+  section_word = 0
+  count = 0
+  tris = []
+  
+  for oneline in filelines[i:]:
+    oneline = oneline.strip()
+    if not oneline: continue
+    if section_word == 0:
+      if oneline != "Triangles":
+        error("Molecule file section is invalid for 3d triangles")
+      section_word = 1
+      continue
+    count += 1
+    words = oneline.split()
+    if int(words[0]) != count:
+      error("Molecule file section is invalid for 3d triangles")
+    tri = Tri((float(words[3]),float(words[4]),float(words[5])),
+              (float(words[6]),float(words[7]),float(words[8])),
+              (float(words[9]),float(words[10]),float(words[11])))
+    tris.append(tri)
+
+  if count != ntris:
+    error("Molecule file section is invalid for 3d triangles")
+    
+  return tris
+  
+# read an STL file with tris
+
+def read_stlfile(filename):
+  filelines = open(filename,"r").readlines()
+
+  if not filelines[0].startswith("solid "):
+    error("STL file first line is invalid")
+  if not filelines[-1].startswith("endsolid "):
+    error("STL file last line is invalid")
+
+  filelines = filelines[1:-1]
+  if (len(filelines) % 7) != 0:
+    error("STL file facet format is invalid")
+
+  tris = []
+
+  iline = 2
+  while iline < len(filelines):
+    v1 = filelines[iline].split()
+    v2 = filelines[iline+1].split()
+    v3 = filelines[iline+2].split()
+    if v1[0] != "vertex" or v2[0] != "vertex" or v3[0] != "vertex":
+      error("STL file vertex format is invalid")
+    tri = Tri((float(v1[1]),float(v1[2]),float(v1[3])),
+              (float(v2[1]),float(v2[2]),float(v2[3])),
+              (float(v3[1]),float(v3[2]),float(v3[3])))
+    tris.append(tri)
+    iline += 7
+    
+  return tris
+
+# create list of unique line end points
+
+def extract_points_2d(lines):
+  points = []
+  hash = {}
+  for line in lines:
+    if line.point1 not in hash:
+      line.p1 = len(points)
+      hash[line.point1] = len(points)
+      pt = line.point1
+      point = Point(pt[0],pt[1],0.0)
+      points.append(point)
+    else: line.p1 = hash[line.point1]
+    if line.point2 not in hash:
+      line.p2 = len(points)
+      hash[line.point2] = len(points)
+      pt = line.point2
+      point = Point(pt[0],pt[1],0.0)
+      points.append(point)
+    else: line.p2 = hash[line.point2]
+  return points
+
+# create list of unique tri corner points
+
+def extract_points_3d(tris):
+  points = []
+  hash = {}
+  for tri in tris:
+    if tri.point1 not in hash:
+      tri.p1 = len(points)
+      hash[tri.point1] = len(points)
+      pt = tri.point1
+      point = Point(pt[0],pt[1],pt[2])
+      points.append(point)
+    else: tri.p1 = hash[tri.point1]
+    if tri.point2 not in hash:
+      tri.p2 = len(points)
+      hash[tri.point2] = len(points)
+      pt = tri.point2
+      point = Point(pt[0],pt[1],pt[2])
+      points.append(point)
+    else: tri.p2 = hash[tri.point2]
+    if tri.point3 not in hash:
+      tri.p3 = len(points)
+      hash[tri.point3] = len(points)
+      pt = tri.point3
+      point = Point(pt[0],pt[1],pt[2])
+      points.append(point)
+    else: tri.p3 = hash[tri.point3]
+  return points
+
+# create list of unique tri edges
+# also create ehash so can search for edges in refine_3d()
+#   key = (p1,p2), value = index into list of edges
+
+def edges_3d(points,tris):
+  hash = {}
+  for i,tri in enumerate(tris):
+    if (tri.p1,tri.p2) in hash: hash[(tri.p1,tri.p2)].append((i,0))
+    elif (tri.p2,tri.p1) in hash: hash[(tri.p2,tri.p1)].append((i,0))
+    else: hash[(tri.p1,tri.p2)] = [(i,0)]
+    if (tri.p2,tri.p3) in hash: hash[(tri.p2,tri.p3)].append((i,1))
+    elif (tri.p3,tri.p2) in hash: hash[(tri.p3,tri.p2)].append((i,1))
+    else: hash[(tri.p2,tri.p3)] = [(i,1)]
+    if (tri.p3,tri.p1) in hash: hash[(tri.p3,tri.p1)].append((i,2))
+    elif (tri.p1,tri.p3) in hash: hash[(tri.p1,tri.p3)].append((i,2))
+    else: hash[(tri.p3,tri.p1)] = [(i,2)]
+
+  edges = []
+  for key,value in hash.items():
+    edge = Edge(key[0],key[1])
+    edge.neigh = [item[0] for item in value]
+    edge.which = [item[1] for item in value]
+    edges.append(edge)
+
+  ehash = {}
+  for iedge,edge in enumerate(edges):
+    ehash[(edge.p1,edge.p2)] = iedge
+    
+  return edges,ehash
+
+# successively refine lines which are too long
+
+def refine_2d(points,lines):
+  sizes = []
+  for iline,line in enumerate(lines):
+    sizes.append((iline,distance(points[line.p1].x,points[line.p2].x)))
+  sizes = sorted(sizes,key=itemgetter(1),reverse=True)
+
+  # loop until no line is too long
+  
+  while sizes[0][1] > thresh:
+    #print(sizes)
+    iline = sizes[0][0]
+    dist = sizes[0][1]
+
+    # add new point
+
+    middle = midpt(points[lines[iline].p1].x,points[lines[iline].p2].x)
+    point = Point(middle[0],middle[1],0.0)
+    points.append(point)
+    npoints = len(points)
+    
+    # mark split line as inactive
+    # add 2 new lines from split line
+
+    lines[iline].active = 0
+
+    newline = Line(lines[iline].point1,middle)
+    newline.p1 = lines[iline].p1
+    newline.p2 = npoints - 1
+    lines.append(newline)
+    inewline1 = len(lines) - 1
+
+    newline = Line(lines[iline].point2,middle)
+    newline.p1 = lines[iline].p2
+    newline.p2 = npoints - 1
+    lines.append(newline)
+    inewline2 = len(lines) - 1
+
+    nlines = len(lines)
+
+    # remove split line from sorted list
+    # add 2 new lines to sorted list in appropriate locations
+
+    del sizes[0]
+
+    newsize = (inewline1,0.5*dist)
+    isize = mybisect(sizes,newsize,sizeindex,1)
+    sizes.insert(isize,newsize)
+
+    newsize = (inewline2,0.5*dist)
+    isize = mybisect(sizes,newsize,sizeindex,1)
+    sizes.insert(isize,newsize)
+
+# successively refine tris while any edge is too long
+
+def refine_3d(points,edges,ehash,tris):
+  sizes = []
+  for iedge,edge in enumerate(edges):
+    sizes.append((iedge,distance(points[edge.p1].x,points[edge.p2].x)))
+  sizes = sorted(sizes,key=itemgetter(1),reverse=True)
+  
+  # loop until no tri edge is too long
+
+  while sizes[0][1] > thresh:
+    iedge = sizes[0][0]
+    dist = sizes[0][1]
+    edges[iedge].active = 0
+
+    # add new point
+
+    middle = midpt(points[edges[iedge].p1].x,points[edges[iedge].p2].x)
+    point = Point(middle[0],middle[1],middle[2])
+    points.append(point)
+    npoints = len(points)
+
+    # loop over tris sharing the split edge
+    #   mark each tri inactive
+    #   add 2 new tris to replace inactive tri
+    #   add new edge between pair of new tris
+    #   reset neighs of non-split and non-new edge for each tri in pair
+    # prev_nedges/ntris = number of edges and tris before adding new ones
+    
+    neigh = edges[iedge].neigh
+    which = edges[iedge].which
+    nedges_prev = len(edges)
+    ntris_prev = len(tris)
+    
+    for itri,iwhich in zip(neigh,which):
+      tris[itri].active = 0
+
+      # NOTE:are not updating neighs in edge correctly
+      
+      if iwhich == 0:
+        newtri = Tri(tris[itri].point1,middle,tris[itri].point3)
+        newtri.p1 = tris[itri].p1
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p3
+        tris.append(newtri)
+
+        if (tris[itri].p3,tris[itri].p1) in ehash:
+          jedge = ehash[(tris[itri].p3,tris[itri].p1)]
+        else: jedge = ehash[(tris[itri].p1,tris[itri].p3)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+        
+        newtri = Tri(tris[itri].point2,middle,tris[itri].point3)
+        newtri.p1 = tris[itri].p2
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p3
+        tris.append(newtri)
+
+        if (tris[itri].p2,tris[itri].p3) in ehash:
+          jedge = ehash[(tris[itri].p2,tris[itri].p3)]
+        else: jedge = ehash[(tris[itri].p3,tris[itri].p2)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+
+        newedge = Edge(tris[itri].p3,npoints-1)
+        newedge.neigh = [len(tris)-2,len(tris)-1]
+        newedge.which = [1,1]
+        edges.append(newedge)
+        ehash[(newedge.p1,newedge.p2)] = len(edges)-1
+
+      elif iwhich == 1:
+        newtri = Tri(tris[itri].point2,middle,tris[itri].point1)
+        newtri.p1 = tris[itri].p2
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p1
+        tris.append(newtri)
+
+        if (tris[itri].p1,tris[itri].p2) in ehash:
+          jedge = ehash[(tris[itri].p1,tris[itri].p2)]
+        else: jedge = ehash[(tris[itri].p2,tris[itri].p1)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+
+        newtri = Tri(tris[itri].point3,middle,tris[itri].point1)
+        newtri.p1 = tris[itri].p3
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p1
+        tris.append(newtri)
+
+        if (tris[itri].p3,tris[itri].p1) in ehash:
+          jedge = ehash[(tris[itri].p3,tris[itri].p1)]
+        else: jedge = ehash[(tris[itri].p1,tris[itri].p3)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+
+        newedge = Edge(tris[itri].p1,npoints-1)
+        newedge.neigh = [len(tris)-2,len(tris)-1]
+        newedge.which = [1,1]
+        edges.append(newedge)
+        ehash[(newedge.p1,newedge.p2)] = len(edges)-1
+
+      elif iwhich == 2:
+        newtri = Tri(tris[itri].point3,middle,tris[itri].point2)
+        newtri.p1 = tris[itri].p3
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p2
+        tris.append(newtri)
+
+        if (tris[itri].p2,tris[itri].p3) in ehash:
+          jedge = ehash[(tris[itri].p2,tris[itri].p3)]
+        else: jedge = ehash[(tris[itri].p3,tris[itri].p2)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+
+        newtri = Tri(tris[itri].point1,middle,tris[itri].point2)
+        newtri.p1 = tris[itri].p1
+        newtri.p2 = npoints - 1
+        newtri.p3 = tris[itri].p2
+        tris.append(newtri)
+        
+        if (tris[itri].p1,tris[itri].p2) in ehash:
+          jedge = ehash[(tris[itri].p1,tris[itri].p2)]
+        else: jedge = ehash[(tris[itri].p2,tris[itri].p1)]
+        index = edges[jedge].neigh.index(itri)
+        edges[jedge].neigh[index] = len(tris)-1
+        edges[jedge].which[index] = 2
+
+        newedge = Edge(tris[itri].p2,npoints-1)
+        newedge.neigh = [len(tris)-2,len(tris)-1]
+        newedge.which = [1,1]
+        edges.append(newedge)
+        ehash[(newedge.p1,newedge.p2)] = len(edges)-1
+
+    # add 2 additional new edges to replace split edge
+    # neigh of each new edge depends on order of points in original tri
+    # both new edges are first edge 0 in all new tris
+
+    newedge1 = Edge(edges[iedge].p1,npoints-1)
+    neigh1 = newedge1.neigh
+    newedge2 = Edge(edges[iedge].p2,npoints-1)
+    neigh2 = newedge2.neigh
+
+    for itri in range(ntris_prev,len(tris)):
+      if edges[iedge].p1 == tris[itri].p1: neigh1.append(itri)
+      else: neigh2.append(itri)
+
+    newedge1.which = (len(neigh1))*[0]
+    newedge2.which = (len(neigh2))*[0]
+
+    edges.append(newedge1)
+    ehash[(newedge1.p1,newedge1.p2)] = len(edges)-1
+    edges.append(newedge2)
+    ehash[(newedge2.p1,newedge2.p2)] = len(edges)-1
+    
+    # remove split edge from sorted list
+    # add all new edges to sorted list in appropriate locations
+
+    del sizes[0]
+
+    for iedge in range(nedges_prev,len(edges)):
+      newsize = (iedge,distance(points[edges[iedge].p1].x,points[edges[iedge].p2].x))
+      isize = mybisect(sizes,newsize,sizeindex,1)
+      sizes.insert(isize,newsize)
+
+# function called by bisect() to return entry field that list is sorted on
+
+def sizeindex(entry):
+  return entry[-1]
+
+# write a new molecule file with lines
+
+def write_molfile_2d(outfile,lines,infile,thresh):
+  nactive = 0
+  for line in lines:
+    if line.active: nactive += 1
+
+  fp = open(outfile,"w")
+  print("LAMMPS molecule file created by refine.py from %s with threshold %g\n" %
+        (infile,thresh),file=fp)
+  print("%d lines\n" % nactive,file=fp)
+  print("Lines\n",file=fp)
+
+  count = 0
+  for line in lines:
+    if not line.active: continue
+    count += 1
+    print("%d %d %d %g %g %g %g" % (count,1,1,
+                                    line.point1[0],line.point1[1],
+                                    line.point2[0],line.point2[1]),file=fp)
+  fp.close()
+  
+# write a new molecule file with tris
+
+def write_molfile_3d(outfile,tris,infile,thresh):
+  nactive = 0
+  for tri in tris:
+    if tri.active: nactive += 1
+
+  fp = open(outfile,"w")
+  print("LAMMPS molecule file created by refine.py from %s with threshold %g\n" %
+        (infile,thresh),file=fp)
+  print("%d triangles\n" % nactive,file=fp)
+  print("Triangles\n",file=fp)
+
+  count = 0
+  for tri in tris:
+    if not tri.active: continue
+    count += 1
+    print("%d %d %d %g %g %g %g %g %g %g %g %g" %
+          (count,1,1,
+           tri.point1[0],tri.point1[1],tri.point1[2],
+           tri.point2[0],tri.point2[1],tri.point2[2],
+           tri.point3[0],tri.point3[1],tri.point3[2]),
+          file=fp)
+  fp.close()
+
+# write a new STL file with tris
+
+def write_stlfile(outfile,tris,infile,thresh):
+  nactive = 0
+  for tri in tris:
+    if tri.active: nactive += 1
+
+  fp = open(outfile,"w")
+  print("solid STL version of %s with threshold %g" %
+        (infile,thresh),file=fp)
+
+  for tri in tris:
+    if not tri.active: continue
+    print("  facet normal 0.0 0.0 0.0",file=fp)
+    print("    outer loop",file=fp)
+    print("      vertex %g %g %g" %
+          (tri.point1[0],tri.point1[1],tri.point1[2]),file=fp)
+    print("      vertex %g %g %g" %
+          (tri.point2[0],tri.point2[1],tri.point2[2]),file=fp)
+    print("      vertex %g %g %g" %
+          (tri.point3[0],tri.point3[1],tri.point3[2]),file=fp)
+    print("    endloop",file=fp)
+    print("  endfacet",file=fp)
+
+  print("endsolid STL version of %s with threshold %g" %
+        (infile,thresh),file=fp)
+  fp.close()
+  
+# ----------
+# main program
+# ----------
+
+# parse command-line args
+
+args = sys.argv[1:]
+narg = len(args)
+
+if narg != 6: error()
+
+dim = int(args[0])
+insource = args[1]
+infile = args[2]
+thresh = float(args[3])
+outsource = args[4]
+outfile = args[5]
+
+if dim != 2 and dim != 3: error("Involid dim argument")
+    
+# read input file
+# lines/tris = list of lines or tris
+
+if insource == "mol" and dim == 2:
+  lines = read_molfile_2d(infile)
+elif insource == "mol" and dim == 3:
+  tris = read_molfile_3d(infile)
+elif insource == "stl" and dim == 3:
+  tris = read_stlfile(infile)
+else:
+  error("Invalid insource argument")
+
+# points = list of unique points
+
+if dim == 2: points = extract_points_2d(lines)
+if dim == 3: points = extract_points_3d(tris)
+
+npoints = len(points)
+if dim == 2:
+  nlines = len(lines)
+if dim == 3:
+  ntris = len(tris)
+
+# edges = list of unique edges for tris
+# ehash = enables search for a p1,p2 edge in edges
+
+if dim == 3: edges,ehash = edges_3d(points,tris)
+
+# perform refinement
+
+if dim == 2: refine_2d(points,lines)
+if dim == 3: refine_3d(points,edges,ehash,tris)
+  
+# write output file
+
+if outsource == "mol" and dim == 2:
+  write_molfile_2d(outfile,lines,infile,thresh)
+elif outsource == "mol" and dim == 3:
+  write_molfile_3d(outfile,tris,infile,thresh)
+elif outsource == "stl" and dim == 3:
+  write_stlfile(outfile,tris,infile,thresh)
+else:
+  error("Invalid outsource argument")