compute bond/local command — LAMMPS documentation

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# compute bond/local command

## Syntax

    compute ID group-ID bond/local value1 value2 ... keyword args ...

- ID, group-ID are documented in compute command

- bond/local = style name of this compute command

- one or more values may be appended

- value = dist or dx or dy or dz or engpot or force or fx or fy or fz or engvib or engrot or engtrans or omega or velvib or v_name or bN

    dist = bond distance
    engpot = bond potential energy
    force = bond force

    dx,dy,dz = components of pairwise distance
    fx,fy,fz = components of bond force
    engvib = bond kinetic energy of vibration
    engrot = bond kinetic energy of rotation
    engtrans = bond kinetic energy of translation
    omega = magnitude of bond angular velocity
    velvib = vibrational velocity along the bond length
    v_name = equal-style variable with name (see below)
    bN = bond style specific quantities for allowed N values

- zero or more keyword/args pairs may be appended

- keyword = set

    set args = dist name
      dist = only currently allowed arg
      name = name of variable to set with distance (dist)

## Examples

    compute 1 all bond/local engpot
    compute 1 all bond/local dist engpot force

    compute 1 all bond/local dist fx fy fz b1 b2

    compute 1 all bond/local dist v_distsq set dist d

## Description

Define a computation that calculates properties of individual bond interactions. The number of datums generated, aggregated across all processors, equals the number of bonds in the system, modified by the group parameter as explained below.

All these properties are computed for the pair of atoms in a bond, whether the two atoms represent a simple diatomic molecule, or are part of some larger molecule.

The value dist is the current length of the bond. The values dx, dy, and dz are the xyz components of the distance between the pair of atoms. This value is always the distance from the atom of lower to the one with the higher id.

The value engpot is the potential energy for the bond, based on the current separation of the pair of atoms in the bond.

The value force is the magnitude of the force acting between the pair of atoms in the bond.

The values fx, fy, and fz are the xyz components of force between the pair of atoms in the bond. For bond styles that apply non-central forces, such as bond_style bpm/rotational, these values only include the \((x,y,z)\) components of the normal force component.

The remaining properties are all computed for motion of the two atoms relative to the center of mass (COM) velocity of the two atoms in the bond.

The value engvib is the vibrational kinetic energy of the two atoms in the bond, which is simply \(\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2,\) where \(v_1\) and \(v_2\) are the magnitude of the velocity of the two atoms along the bond direction, after the COM velocity has been subtracted from each.

The value engrot is the rotational kinetic energy of the two atoms in the bond, which is simply \(\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2,\) where \(v_1\) and \(v_2\) are the magnitude of the velocity of the two atoms perpendicular to the bond direction, after the COM velocity has been subtracted from each.

The value engtrans is the translational kinetic energy associated with the motion of the COM of the system itself, namely \(\frac12(m_1+m_2) V_{\mathrm{cm}}^2\), where Vcm = magnitude of the velocity of the COM.

Note that these three kinetic energy terms are simply a partitioning of the summed kinetic energy of the two atoms themselves. That is, the total kinetic energy is \(\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2\) = engvib + engrot + engtrans, where \(v_1\) and \(v_2\) are the magnitude of the velocities of the two atoms, without any adjustment for the COM velocity.

The value omega is the magnitude of the angular velocity of the two atoms around their COM position.

The value velvib is the magnitude of the relative velocity of the two atoms in the bond towards each other. A negative value means the two atoms are moving toward each other; a positive value means they are moving apart.

The value v_name can be used together with the set keyword to compute a user-specified function of the bond distance. The name specified for the v_name value is the name of an equal-style variable which should evaluate a formula based on a variable which will store the bond distance. This other variable must be an internal-style variable defined in the input script; its initial numeric value can be anything. It must be an internal-style variable, because this command resets its value directly. The set keyword is used to identify the name of this other variable associated with theta.

As an example, these commands can be added to the bench/in.rhodo script to compute the length\(^2\) of every bond in the system and output the statistics in various ways:

    variable d internal 0.0
    variable dsq equal v_d*v_d

    compute 1 all property/local batom1 batom2 btype
    compute 2 all bond/local engpot dist v_dsq set dist d
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]

    compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]

    fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo

The dump local command will output the energy, length, and length\(^2\) for every bond in the system. The thermo_style command will print the average of those quantities via the compute reduce command with thermo output, and the fix ave/histo command will histogram the length\(^2\) values and write them to a file.

A bond style may define additional bond quantities which can be accessed as b1 to bN, where N is defined by the bond style. Most bond styles do not define any additional quantities, so N = 0. An example of ones that do are the BPM bond styles which store the reference state between two particles. See individual bond styles for details.

When using bN with bond style hybrid, the output will be the Nth quantity from the sub-style that computes the bonded interaction (based on bond type). If that sub-style does not define a bN, the output will be 0.0. The maximum allowed N is the maximum number of quantities provided by any sub-style.

The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. Any bonds that have been broken (see the bond_style command) by setting their bond type to 0 are not included. Bonds that have been turned off (see the fix shake or delete_bonds commands) by setting their bond type negative are written into the file, but their energy will be 0.0.

Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. For example, bond output from the compute property/local command can be combined with data from this command and output by the dump local command in a consistent way.

Here is an example of how to do this:

    compute 1 all property/local btype batom1 batom2
    compute 2 all bond/local dist engpot
    dump 1 all local 1000 tmp.dump index c_1[*] c_2[*]

## Output info

This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the array is the number of bonds. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. 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 output for dist will be in distance units. The output for velvib will be in velocity units. The output for omega will be in velocity/distance units. The output for engtrans, engvib, engrot, and engpot will be in energy units. The output for force will be in force units.

## Restrictions

> none

## Related commands

dump local, compute property/local

## Default

none