Updating gitignore

doc/src/dump_modify.rst

@@ -66,7 +66,7 @@ Syntax
        *unwrap* arg = *yes* or *no*
 
 * these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
-* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
+* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
 
   .. parsed-literal::
 
@@ -113,6 +113,9 @@ Syntax
          rate = target bitrate for movie in kbps
        *framerate* arg = fps
          fps = frames per second for movie
+       *header* arg = *yes* or *no*
+         *yes* to write the header
+         *no* to not write the header
 
 * these keywords apply only to the */gz* and */zstd* dump styles
 * keyword = *compression_level*
@@ -977,6 +980,13 @@ images less frequently.
 
 ----------
 
+The *header* keyword toggles whether the dump file will include a header.
+Excluding a header will reduce the size of the dump file for fixes such as 
+:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
+typically written to the header.
+
+----------
+
 The COMPRESS package offers both GZ and Zstd compression variants of styles
 atom, custom, local, cfg, and xyz. When using these styles the compression
 level can be controlled by the :code:`compression_level` parameter. File names

doc/src/fix_pair_tracker.rst

@@ -0,0 +1,121 @@
+.. index:: fix pair/tracker
+
+fix pair/tracker command
+===================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* pair/tracker = style name of this fix command
+* N = prepare data for output every this many timesteps
+* one or more attributes may be appended
+
+  .. parsed-literal::
+
+       possible attributes = id1 id2 time/created time/broken time/total
+                             rmin rave x y z
+
+  .. parsed-literal::
+
+          id1, id2 = IDs of 2 atoms in each pair interaction
+          time/created = the time the 2 atoms began interacting
+          time/broken = the time the 2 atoms stopped interacting
+          time/total = the total time the 2 atoms interacted
+          r/min = the minimum radial distance between the 2 atoms during the interaction
+          r/ave = the average radial distance between the 2 atoms during the interaction
+          x, y, z = the center of mass position of the 2 atoms when they stopped interacting
+
+* zero or more keyword/value pairs may be appended
+* keyword = *time/min* or *type/include*
+
+  .. parsed-literal::
+
+       *time/min* value = T
+         T = minimum interaction time 
+       *type/include* value = arg1 arg2
+         arg = separate lists of types (see below)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all pair/tracker 1000 id1 id2 tmin 100
+   fix 1 all pair/tracker 1000 time/created time/broken type 1 * type 2 3,4
+
+Description
+"""""""""""
+
+Tracks properties of pairwise interactions between two atoms and records data
+whenever the atoms move beyond the interaction cutoff or the interaction breaks. 
+Must be used in conjuction with :doc:`pair tracker <pair_tracker>`.
+Data is accumulated over a span of *N* timesteps after which it is cleared
+The number of datums generated, aggregated across all processors, equals 
+the number of broken interactions. Interactions are only included if both
+atoms are in the included in the specified fix group. Additional filters can be
+applied using the *tmin* or *type* keywords described below.
+
+.. note::
+
+   For extremely long-lived interactions, the calculation of *r/ave* may not be 
+   correct due to double overflow.
+
+The *time/min* keyword defines a minimum amount of time atoms have to be interacting
+to save data. This can be used to censor short-lived interactions. The *type/include*
+keyword filters interactions based on the types of the two atoms. Data is 
+only saved for interactions between atoms with types in the two lists. 
+Each list consists of a series of type
+ranges separated by commas. The range can be specified as a
+single numeric value, or a wildcard asterisk can be used to specify a range
+of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+example, if M = the number of atom types, then an asterisk with no numeric
+values means all types from 1 to M.  A leading asterisk means all types
+from 1 to n (inclusive).  A trailing asterisk means all types from n to M
+(inclusive).  A middle asterisk means all types from m to n (inclusive).
+Note that all atom types must be included in exactly one of the N collections.
+Multiple *type/include* keywords may be added.
+
+----------
+
+Restart, fix_modify, 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 parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+Output info
+"""""""""""
+
+This compute calculates a local vector or local array depending on the
+number of input values.  The length of the vector or number of rows in
+the array is the number of bonds, angles, etc.  If a single input is
+specified, a local vector is produced.  If two or more inputs are
+specified, a local array is produced where the number of columns = the
+number of inputs.  The vector or array can be accessed by any command
+that uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+options.
+
+The vector or array values will be doubles that correspond to the
+specified attribute.
+
+Restrictions
+""""""""""""
+ none
+ 
+Related commands
+""""""""""""""""
+
+:doc:`pair tracker <pair_tracker>`
+
+Default
+"""""""
+
+none

doc/src/pair_granular.rst

@@ -665,12 +665,6 @@ then LAMMPS will use that cutoff for the specified atom type
 combination, and automatically set pairwise cutoffs for the remaining
 atom types.
 
-If two particles are moving away from each other while in contact, there
-is a possibility that the particles could experience an effective attractive
-force due to damping. If the *limit_damping* keyword is used, this option
-will zero out the normal component of the force if there is an effective
-attractive force. This keyword cannot be used with the JKR or DMT models.
-
 ----------
 
 .. include:: accel_styles.rst

doc/src/pair_tracker.rst

@@ -0,0 +1,92 @@
+.. index:: pair_style tracker
+
+pair_style tracker command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style tracker keyword
+
+* zero or more keyword/arg pairs may be appended
+* keyword = *finite*
+
+  .. parsed-literal::
+
+      *finite* pair style uses atomic diameters to identify contacts  
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay tracker ...
+   pair_coeff 1 1 tracker 2.0
+
+   pair_style hybrid/overlay tracker finite ...
+   pair_coeff * * tracker
+   
+   fix 1 all pair/tracker 1000 time/created time/broken
+   dump 1 all local 1000 dump.local f_1[1] f_1[2]
+   dump_modify 1 write_header no
+
+Description
+"""""""""""
+
+Style *tracker* monitors information about pairwise interactions.
+It does not calculate any forces on atoms and should be used with  
+:doc:`pair hybrid/overlay <pair_hybrid>` to combine with a regularly
+used pair style. Style *tracker*  must be used in conjunction with about
+:doc:`fix pair_tracker <fix_pair_tracker>` which contains information on 
+what data can be output.
+
+If the *finite* keyword is not defined, the following coefficients must be 
+defined for each pair of atom types via the :doc:`pair_coeff <pair_coeff>` 
+command as in the examples above, or in the data file or restart files 
+read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+commands, or by mixing as described below:
+
+* cutoff (distance units)
+
+If the *finite* keyword is defined, no coeffients may be defined. 
+Alternatively, interactions are defined if finite particles overlap.
+
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, the cutoff coefficient and cutoff
+distance for this pair style can be mixed.  The cutoff is always mixed via a
+*geometric* rule.  The cutoff is mixed according to the pair_modify
+mix value.  The default mix value is *geometric*\ .  See the
+"pair_modify" command for details.
+  
+This pair style writes its information to :doc:`binary restart files <restart>`, so 
+pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+The :doc:`pair_modify <pair_modify>` shift, table, and tail options
+are not relevant for this pair style.
+
+----------
+
+Restrictions
+""""""""""""
+
+A corresponding :doc:`fix pair_tracker <fix_pair_tracker>` must be defined
+to use this pair style.
+
+This pairstyle is currently incompatible with granular pairstyles that extend
+beyond the contact (e.g. JKR and DMT).
+
+Related commands
+""""""""""""""""
+
+:doc:`fix pair_tracker <fix_pair_tracker>`
+
+Default
+"""""""
+
+none

src/.gitignore

@@ -704,6 +704,8 @@
 /fix_orient_eco.h
 /fix_orient_fcc.cpp
 /fix_orient_fcc.h
+/fix_pair_tracker.cpp
+/fix_pair_tracker.h
 /fix_peri_neigh.cpp
 /fix_peri_neigh.h
 /fix_phonon.cpp
@@ -1149,6 +1151,8 @@
 /pair_tip4p_long.h
 /pair_tip4p_long_soft.cpp
 /pair_tip4p_long_soft.h
+/pair_tracker.h
+/pair_tracker.cpp
 /pair_tri_lj.cpp
 /pair_tri_lj.h
 /pair_yukawa_colloid.cpp