pair_style tracker command

Syntax

pair_style tracker fix_ID N keyword values attribute1 attribute2 ...
  • fix_ID = ID of associated internal fix to store data

  • N = prepare data for output every this many timesteps

  • zero or more keywords may be appended

  • keyword = finite or time/min or type/include

    finite value = none
       pair style uses atomic diameters to identify contacts
    time/min value = T
       T = minimum number of timesteps of interaction
    type/include value = list1 list2
       list1,list2 = separate lists of types (see below)
  • one or more attributes may be appended

    possible attributes = id1 id2 time/created time/broken time/total
                          r/min r/ave x y z
    
    id1, id2 = IDs of the 2 atoms in each pair interaction
    time/created = the timestep that the 2 atoms began interacting
    time/broken = the timestep that the 2 atoms stopped interacting
    time/total = the total number of timesteps the 2 atoms interacted
    r/min = the minimum radial distance between the 2 atoms during the interaction (distance units)
    r/ave = the average radial distance between the 2 atoms during the interaction (distance units)
    x, y, z = the center of mass position of the 2 atoms when they stopped interacting (distance units)
    

Examples

pair_style hybrid/overlay tracker myfix 1000 id1 id2 type/include 1 * type/include 2 3,4  lj/cut 2.5
pair_coeff 1 1 tracker 2.0

pair_style hybrid/overlay tracker myfix 1000 finite x y z time/min 100 granular
pair_coeff * * tracker

dump 1 all local 1000 dump.local f_myfix[1] f_myfix[2] f_myfix[3]
dump_modify 1 write_header no

Description

Style tracker monitors information about pairwise interactions. It does not calculate any forces on atoms. Pair hybrid/overlay can be used to combine this pair style with any other pair style, as shown in the examples above.

At each timestep, if two neighboring atoms move beyond the interaction cutoff, pairwise data is processed and transferred to an internal fix labeled fix_ID. This allows the local data to be accessed by other LAMMPS commands. Additional filters can be applied using the time/min or type/include keywords described below. Note that this is the interaction cutoff defined by this pair style, not the short-range cutoff defined by the pair style that is calculating forces on atoms.

Following any optional keyword/value arguments, a list of one or more attributes is specified. These include the IDs of the two atoms in the pair. The other attributes for the pair of atoms are the duration of time they were “interacting” or at the point in time they started or stopped interacting. In this context, “interacting” means the time window during which the two atoms were closer than the interaction cutoff distance. The attributes for time/* refer to timesteps.

Data is continuously accumulated by the internal fix over intervals of N timesteps. At the end of each interval, all of the saved accumulated data is deleted to make room for new data. Individual datum may therefore persist anywhere between 1 to N timesteps depending on when they are saved. This data can be accessed using the fix_ID and a dump local command. To ensure all data is output, the dump frequency should correspond to the same interval of N timesteps. A dump frequency of an integer multiple of N can be used to regularly output a sample of the accumulated data.


The following optional keywords may be used.

If the finite keyword is not used, the following coefficients must be defined for each pair of atom types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below:

  • cutoff (distance units)

If the finite keyword is used, there are no additional coefficients to set for each pair of atom types via the pair_coeff command. Interaction cutoffs are instead calculated based on the diameter of finite particles. However you must still use the pair_coeff for all atom types. For example the command

pair_coeff * *

should be used.

The time/min keyword sets a minimum amount of time that an interaction must persist to be included. This setting 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 whose two atom types appear in list1 and list2. Atom type 1 must be in list1 and atom type 2 in list2. Or vice versa.

Each type list consists of a series of type ranges separated by commas. Each 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 the type/include keyword can be specified multiple times.

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 binary restart files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file.

The pair_modify shift, table, and tail options are not relevant for this pair style.

The accumulated data is not written to restart files and should be output before a restart file is written to avoid missing data.

The internal fix 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 recorded, lost interactions. 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 Howto output page for an overview of LAMMPS output options.

The vector or array will be floating point values that correspond to the specified attribute.


Restrictions

This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

This pair style is currently incompatible with granular pair styles that extend beyond the contact (e.g. JKR and DMT).

Default

none