compute temp/chunk command — LAMMPS documentation

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# compute temp/chunk command

## Syntax

    compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ...

- ID, group-ID are documented in compute command

- temp/chunk = style name of this compute command

- chunkID = ID of compute chunk/atom command

- zero or more values can be listed as value1,value2,etc.

- value = temp or kecom or internal

      temp = temperature of each chunk
      kecom = kinetic energy of each chunk based on velocity of center of mass
      internal = internal kinetic energy of each chunk

- zero or more keyword/value pairs may be appended

- keyword = com or bias or adof or cdof

      com value = yes or no
        yes = subtract center-of-mass velocity from each chunk before calculating temperature
        no = do not subtract center-of-mass velocity
      bias value = bias-ID
        bias-ID = ID of a temperature compute that removes a velocity bias
      adof value = dof_per_atom
        dof_per_atom = define this many degrees-of-freedom per atom
      cdof value = dof_per_chunk
        dof_per_chunk = define this many degrees-of-freedom per chunk

## Examples

    compute 1 fluid temp/chunk molchunk
    compute 1 fluid temp/chunk molchunk temp internal
    compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0

## Description

Define a computation that calculates the temperature of a group of atoms that are also in chunks, after optionally subtracting out the center-of-mass velocity of each chunk. By specifying optional values, it can also calculate the per-chunk temperature or energies of the multiple chunks of atoms.

In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the compute chunk/atom and Howto chunk doc pages for details of how chunks can be defined and examples of how they can be used to measure properties of a system.

The temperature is calculated by the formula

\[\text{KE} = \frac{\text{DOF}}{2} k_B T,\]

where KE is the total kinetic energy of all atoms assigned to chunks (sum of \(\frac12 m v^2\)), DOF is the the total number of degrees of freedom for those atoms, \(k_B\) is Boltzmann constant, and \(T\) is the absolute temperature.

The DOF is calculated as \(N\times\)adof + \(N_\text{chunk}\times\)cdof, where \(N\) is the number of atoms contributing to the kinetic energy, adof is the number of degrees of freedom per atom, and cdof is the number of degrees of freedom per chunk. By default, adof = 2 or 3 = dimensionality of system, as set via the dimension command, and cdof = 0.0. This gives the usual formula for temperature.

A symmetric tensor, stored as a six-element vector, is also calculated by this compute. The formula for the components of the tensor is the same as the above expression for \(E_\mathrm{kin}\), except that the 1/2 factor is NOT included and the \(v_i^2\) is replaced by \(v_{i,x} v_{i,y}\) for the \(xy\) component, and so on. Note that because it lacks the 1/2 factor, these tensor components are twice those of the traditional kinetic energy tensor. The six components of the vector are ordered \(xx\), \(yy\), \(zz\), \(xy\), \(xz\), \(yz\).

Note that the number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed the atoms may be dynamically assigned to chunks. Thus there is no need to use the dynamic option of the compute_modify command for this compute style.

If any optional values are specified, then per-chunk quantities are also calculated and stored in a global array, as described below.

The temp value calculates the temperature for each chunk by the formula

\[\text{KE} = \frac{\text{DOF}}{2} k_B T,\]

where KE is the total kinetic energy of the chunk of atoms (sum of \(\frac12 m v^2\)), DOF is the total number of degrees of freedom for all atoms in the chunk, \(k_B\) is the Boltzmann constant, and \(T\) is the absolute temperature.

The number of degrees of freedom (DOF) in this case is calculated as \(N\times\)adof + cdof, where \(N\) is the number of atoms in the chunk, adof is the number of degrees of freedom per atom, and cdof is the number of degrees of freedom per chunk. By default, cdof = 2 or 3 = dimensionality of system, as set via the dimension command, and cdof = 0.0. This gives the usual formula for temperature.

The kecom value calculates the kinetic energy of each chunk as if all its atoms were moving with the velocity of the center-of-mass of the chunk.

The internal value calculates the internal kinetic energy of each chunk. The interal KE is summed over the atoms in the chunk using an internal “thermal” velocity for each atom, which is its velocity minus the center-of-mass velocity of the chunk.

Note that currently the global and per-chunk temperatures calculated by this compute only include translational degrees of freedom for each atom. No rotational degrees of freedom are included for finite-size particles. Also no degrees of freedom are subtracted for any velocity bias or constraints that are applied, such as compute temp/partial, or fix shake or fix rigid. This is because those degrees of freedom (e.g., a constrained bond) could apply to sets of atoms that are both included and excluded from a specific chunk, and hence the concept is somewhat ill-defined. In some cases, you can use the adof and cdof keywords to adjust the calculated degrees of freedom appropriately, as explained below.

Note that the per-chunk temperature calculated by this compute and the fix ave/chunk temp command can be different. This compute calculates the temperature for each chunk for a single snapshot. Fix ave/chunk can do that but can also time average those values over many snapshots, or it can compute a temperature as if the atoms in the chunk on different timesteps were collected together as one set of atoms to calculate their temperature. This compute allows the center-of-mass velocity of each chunk to be subtracted before calculating the temperature; fix ave/chunk does not.

Note

Only atoms in the specified group contribute to the calculations performed by this compute. The compute chunk/atom command defines its own group; atoms will have a chunk ID = 0 if they are not in that group, signifying they are not assigned to a chunk, and will thus also not contribute to this calculation. You can specify the “all” group for this command if you simply want to include atoms with non-zero chunk IDs.

The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the fix ave/time command, for example:

    compute cc1 all chunk/atom molecule
    compute myChunk all temp/chunk cc1 temp
    fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector

The keyword/value option pairs are used in the following ways.

The com keyword can be used with a value of yes to subtract the velocity of the center-of-mass (VCM) for each chunk from the velocity of the atoms in that chunk, before calculating either the global or per-chunk temperature. This can be useful if the atoms are streaming or otherwise moving collectively, and you wish to calculate only the thermal temperature. This per-chunk VCM bias can be used in other fixes and computes that can incorporate a temperature bias. If this compute is used as a temperature bias in other commands then this bias is subtracted from each atom, the command runs with the remaining thermal velocities, and then the bias is added back in. This includes thermostatting fixes like fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin, and computes like compute stress/atom and compute pressure. See the input script in examples/stress_vcm for an example of how to use the com keyword in conjunction with compute stress/atom to create a stress profile of a rigid body while removing the overall motion of the rigid body.

For the bias keyword, bias-ID refers to the ID of a temperature compute that removes a “bias” velocity from each atom. This also allows calculation of the global or per-chunk temperature using only the thermal temperature of atoms in each chunk after the translational kinetic energy components have been altered in a prescribed way (e.g., to remove a velocity profile). It also applies to the calculation of the other per-chunk values, such as kecom or internal, which involve the center-of-mass velocity of each chunk, which is calculated after the velocity bias is removed from each atom. Note that the temperature compute will apply its bias globally to the entire system, not on a per-chunk basis.

The adof and cdof keywords define the values used in the degree of freedom (DOF) formulas used for the global or per-chunk temperature, as described above. They can be used to calculate a more appropriate temperature for some kinds of chunks. Here are three examples:

If spatially binned chunks contain some number of water molecules and fix shake is used to make each molecule rigid, then you could calculate a temperature with six degrees of freedom (DOF) (three translational, three rotational) per molecule by setting adof to 2.0.

If compute temp/partial is used with the bias keyword to only allow the x component of velocity to contribute to the temperature, then adof = 1.0 would be appropriate.

If each chunk consists of a large molecule, with some number of its bonds constrained by fix shake or the entire molecule by fix rigid/small, adof = 0.0 and cdof could be set to the remaining degrees of freedom for the entire molecule (entire chunk in this case; i.e., 6 for 3d, or 3 for 2d, for a rigid molecule).

## Output info

This compute calculates a global scalar (the temperature) and a global vector of length 6 (symmetric tensor), which can be accessed by indices 1–6. These values can be used by any command that uses global scalar or vector values from a compute as input. See the Howto output page for an overview of LAMMPS output options.

This compute also optionally calculates a global array, if one or more of the optional values are specified. The number of rows in the array is the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns is the number of specified values (1 or more). These values can be accessed by any command that uses global array values from a compute as input. Again, see the Howto output doc page for an overview of LAMMPS output options.

The scalar value calculated by this compute is “intensive”. The vector values are “extensive”. The array values are “intensive”.

The scalar value is in temperature units. The vector values are in energy units. The array values will be in temperature units for the temp value, and in energy units for the kecom and internal values.

## Restrictions

The com and bias keywords cannot be used together.

## Related commands

compute temp, fix ave/chunk temp

## Default

The option defaults are com no, no bias, adof = dimensionality of the system (2 or 3), and cdof = 0.0.