forked from lijiext/lammps
235 lines
10 KiB
Plaintext
235 lines
10 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute temp/chunk command :h3
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[Syntax:]
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compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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temp/chunk = style name of this compute command :l
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chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
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zero or more values can be listed as value1,value2,etc :l
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value = {temp} or {kecom} or {internal} :l
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temp = temperature of each chunk
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kecom = kinetic energy of each chunk based on velocity of center of mass
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internal = internal kinetic energy of each chunk :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {com} or {bias} or {adof} or {cdof} :l
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{com} value = {yes} or {no}
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yes = subtract center-of-mass velocity from each chunk before calculating temperature
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no = do not subtract center-of-mass velocity
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{bias} value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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{adof} value = dof_per_atom
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dof_per_atom = define this many degrees-of-freedom per atom
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{cdof} value = dof_per_chunk
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dof_per_chunk = define this many degrees-of-freedom per chunk :pre
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:ule
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[Examples:]
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compute 1 fluid temp/chunk molchunk
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compute 1 fluid temp/chunk molchunk temp internal
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compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre
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[Description:]
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Define a computation that calculates the temperature of a group of
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atoms that are also in chunks, after optionally subtracting out the
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center-of-mass velocity of each chunk. By specifying optional values,
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it can also calulate the per-chunk temperature or energies of the
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multiple chunks of atoms.
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In LAMMPS, chunks are collections of atoms defined by a "compute
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chunk/atom"_compute_chunk_atom.html command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the "compute
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chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
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23"_Section_howto.html#howto_23 for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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The temperature is calculated by the formula KE = DOF k T, where KE =
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total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
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v^2), DOF = the total number of degrees of freedom for those atoms, k
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= Boltzmann constant, and T = temperature.
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The DOF is calculated as N*adof + Nchunk*cdof, where N = number of
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atoms contributing to the KE, adof = degrees of freedom per atom, and
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cdof = degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the "dimension"_dimension.html
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command, and cdof = 0.0. This gives the usual formula for
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temperature.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.
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Note that the number of atoms contributing to the temperature is
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calculated each time the temperature is evaluated since it is assumed
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the atoms may be dynamically assigned to chunks. Thus there is no
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need to use the {dynamic} option of the
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"compute_modify"_compute_modify.html command for this compute style.
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If any optional values are specified, then per-chunk quantities are
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also calculated and stored in a global array, as described below.
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The {temp} value calculates the temperature for each chunk by the
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formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk
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of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of
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freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.
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The DOF in this case is calculated as N*adof + cdof, where N = number
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of atoms in the chunk, adof = degrees of freedom per atom, and cdof =
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degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the "dimension"_dimension.html
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command, and cdof = 0.0. This gives the usual formula for
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temperature.
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The {kecom} value calculates the kinetic energy of each chunk as if
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all its atoms were moving with the velocity of the center-of-mass of
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the chunk.
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The {internal} value calculates the internal kinetic energy of each
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chunk. The interal KE is summed over the atoms in the chunk using an
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internal "thermal" velocity for each atom, which is its velocity minus
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the center-of-mass velocity of the chunk.
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:line
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Note that currently the global and per-chunk temperatures calculated
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by this compute only include translational degrees of freedom for each
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atom. No rotational degrees of freedom are included for finite-size
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particles. Also no degrees of freedom are subtracted for any velocity
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bias or constraints that are applied, such as "compute
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temp/partial"_compute_temp_partial.html, or "fix shake"_fix_shake.html
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or "fix rigid"_fix_rigid.html. This is because those degrees of
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freedom (e.g. a constrained bond) could apply to sets of atoms that
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are both included and excluded from a specific chunk, and hence the
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concept is somewhat ill-defined. In some cases, you can use the
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{adof} and {cdof} keywords to adjust the calculated degress of freedom
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appropriately, as explained below.
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Note that the per-chunk temperature calulated by this compute and the
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"fix ave/chunk temp"_fix_ave_chunk.html command can be different.
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This compute calculates the temperature for each chunk for a single
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snapshot. Fix ave/chunk can do that but can also time average those
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values over many snapshots, or it can compute a temperature as if the
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atoms in the chunk on different timesteps were collected together as
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one set of atoms to calculate their temperature. This compute allows
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the center-of-mass velocity of each chunk to be subtracted before
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calculating the temperature; fix ave/chunk does not.
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IMPORTANT NOTE: Only atoms in the specified group contribute to the
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calculations performed by this compute. The "compute
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chunk/atom"_compute_chunk_atom.html command defines its own group;
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atoms will have a chunk ID = 0 if they are not in that group,
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signifying they are not assigned to a chunk, and will thus also not
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contribute to this calculation. You can specify the "all" group for
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this command if you simply want to include atoms with non-zero chunk
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IDs.
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The simplest way to output the per-chunk results of the compute
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temp/chunk calculation to a file is to use the "fix
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ave/time"_fix_ave_time.html command, for example:
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compute cc1 all chunk/atom molecule
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compute myChunk all temp/chunk cc1 temp
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
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:line
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The keyword/value option pairs are used in the following ways.
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The {com} keyword can be used with a value of {yes} to subtract the
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velocity of the center-of-mass for each chunk from the velocity of the
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atoms in that chunk, before calculating either the global or per-chunk
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temperature. This can be useful if the atoms are streaming or
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otherwise moving collectively, and you wish to calculate only the
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thermal temperature.
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For the {bias} keyword, {bias-ID} refers to the ID of a temperature
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compute that removes a "bias" velocity from each atom. This also
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allows calculation of the global or per-chunk temperature using only
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the thermal temperature of atoms in each chunk after the translational
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kinetic energy components have been altered in a prescribed way,
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e.g. to remove a velocity profile. It also applies to the calculation
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of the other per-chunk values, such as {kecom} or {internal}, which
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involve the center-of-mass velocity of each chunk, which is calculated
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after the velocity bias is removed from each atom. Note that the
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temperature compute will apply its bias globally to the entire system,
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not on a per-chunk basis.
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The {adof} and {cdof} keywords define the values used in the degree of
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freedom (DOF) formulas used for the global or per-chunk temperature,
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as described above. They can be used to calculate a more appropriate
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temperature for some kinds of chunks. Here are 3 examples.
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If spatially binned chunks contain some number of water molecules and
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"fix shake"_fix_shake.html is used to make each molecule rigid, then
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you could calculate a temperature with 6 degrees of freedom (DOF) (3
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translational, 3 rotational) per molecule by setting {adof} to 2.0.
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If "compute temp/partial"_compute_temp_partial.html is used with the
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{bias} keyword to only allow the x component of velocity to contribute
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to the temperature, then {adof} = 1.0 would be appropriate. If each
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chunk consists of a large molecule, with some number of its bonds
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constrained by "fix shake"_fix_shake.html or the entire molecule by
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"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the
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remaining degrees of freedom for the entire molecule (entire chunk in
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this case).
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:line
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[Output info:]
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This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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This compute also optionally calculates a global array, if one or more
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of the optional values are specified. The number of rows in the array
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= the number of chunks {Nchunk} as calculated by the specified
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"compute chunk/atom"_compute_chunk_atom.html command. The number of
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columns is the number of specifed values (1 or more). These values
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can be accessed by any command that uses global array values from a
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compute as input. Again, see "Section_howto
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15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The scalar value calculated by this compute is "intensive". The
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vector values are "extensive". The array values are "intensive".
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The scalar value will be in temperature "units"_units.html. The
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vector values will be in energy "units"_units.html. The array values
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will be in temperature "units"_units.html for the {temp} value, and in
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energy "units"_units.html for the {kecom} and {internal} values.
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[Restrictions:]
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The {com} and {bias} keywords cannot be used together.
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[Related commands:]
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"compute temp"_compute_temp.html, "fix ave/chunk
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temp"_fix_ave_chunk.html
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[Default:]
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The option defaults are com no, no bias, adof = dimensionality of the
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system (2 or 3), and cdof = 0.0.
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