bond_style bpm/spring command

Syntax

bond_style bpm/spring keyword value attribute1 attribute2 ...
  • optional keyword = overlay/pair or store/local or smooth

    store/local values = fix_ID N attributes ...
       * fix_ID = ID of associated internal fix to store data
       * N = prepare data for output every this many timesteps
       * attributes = zero or more of the below attributes may be appended
    
         id1, id2 = IDs of 2 atoms in the bond
         time = the timestep the bond broke
         x, y, z = the center of mass position of the 2 atoms when the bond broke (distance units)
         x/ref, y/ref, z/ref = the initial center of mass position of the 2 atoms (distance units)
    
    overlay/pair value = none
       bonded particles will still interact with pair forces
    
    smooth value = yes or no
       smooths bond forces near the breaking point

Examples

bond_style bpm/spring
bond_coeff 1 1.0 0.05 0.1

bond_style bpm/spring myfix 1000 time id1 id2
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
dump_modify 1 write_header no

Description

The bpm/spring bond style computes forces and torques based on deviations from the initial reference state of the two atoms. The reference state is stored by each bond when it is first computed in the setup of a run. Data is then preserved across run commands and is written to binary restart files such that restarting the system will not reset the reference state of a bond.

This bond style only applies central-body forces which conserve the translational and rotational degrees of freedom of a bonded set of particles. The force has a magnitude of

\[F = k (r - r_0) w\]

where \(k_r\) is a stiffness, \(r\) is the current distance and \(r_0\) is the initial distance between the two particles, and \(w\) is an optional smoothing factor discussed below. Bonds will break at a strain of \(\epsilon_c\). This is done by setting by setting its type to 0 such that forces are no longer computed.

An additional damping force is applied to the bonded particles. This forces is proportional to the difference in the normal velocity of particles using a similar construction as dissipative particle dynamics ((Groot)):

\[F_D = - \gamma w (\hat{r} \bullet \vec{v})\]

where \(\gamma\) is the damping strength, \(\hat{r}\) is the radial normal vector, and \(\vec{v}\) is the velocity difference between the two particles.

The smoothing factor \(w\) can be added or removed using the smooth keyword. It is constructed such that forces smoothly go to zero, avoiding discontinuities, as bonds approach the critical strain

\[w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .\]

The following coefficients must be defined for each bond type via the bond_coeff command as in the example above, or in the data file or restart files read by the read_data or read_restart commands:

  • \(k\) (force/distance units)

  • \(\epsilon_c\) (unit less)

  • \(\gamma\) (force/velocity units)

By default, pair forces are not calculated between bonded particles. Pair forces can alternatively be overlaid on top of bond forces using the overlay/pair keyword. These settings require specific special_bonds settings described in the restrictions. Further details can be found in the :doc: how to <Howto_BPM> page on BPMs.

If the store/local keyword is used, this fix will track bonds that break during the simulation. Whenever a bond breaks, data is processed and transferred to an internal fix labeled fix_ID. This allows the local data to be accessed by other LAMMPS commands. 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 bond. The other attributes for the two atoms include the timestep during which the bond broke and the current/initial center of mass position of the two atoms.

Data is continuously accumulated 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.

Note that when unbroken bonds are dumped to a file via the dump local command, bonds with type 0 (broken bonds) are not included. The delete_bonds command can also be used to query the status of broken bonds or permanently delete them, e.g.:

delete_bonds all stats
delete_bonds all bond 0 remove

Restart and other info

This bond style writes the reference state of each bond to binary restart files. Loading a restart file will properly resume bonds.

The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these dissipative potentials.

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 bond style can only be used if LAMMPS was built with the BPM package. See the Build package doc page for more info.

By default if pair interactions are to be disabled, this bond style requires setting

special_bonds lj 0 1 1 coul 1 1 1

and newton must be set to bond off. If the overlay/pair option is used, this bond style alternatively requires setting

special_bonds lj/coul 1 1 1

Default

The option defaults are smooth = yes


(Groot) Groot and Warren, J Chem Phys, 107, 4423-35 (1997).