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< title > compute temp/chunk command — LAMMPS 17 Dec 2015 documentation< / title >
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< li > compute temp/chunk command< / li >
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< div class = "section" id = "compute-temp-chunk-command" >
< span id = "index-0" > < / span > < h1 > compute temp/chunk command< a class = "headerlink" href = "#compute-temp-chunk-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > temp/chunk = style name of this compute command< / li >
< li > chunkID = ID of < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command< / li >
< li > zero or more values can be listed as value1,value2,etc< / li >
< li > value = < em > temp< / em > or < em > kecom< / em > or < em > internal< / em > < / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > temp = temperature of each chunk
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kecom = kinetic energy of each chunk based on velocity of center of mass
internal = internal kinetic energy of each chunk
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< / pre > < / div >
< / div >
< ul class = "simple" >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > com< / em > or < em > bias< / em > or < em > adof< / em > or < em > cdof< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > com< / em > value = < em > yes< / em > or < em > no< / em >
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yes = subtract center-of-mass velocity from each chunk before calculating temperature
no = do not subtract center-of-mass velocity
< em > bias< / em > value = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias
< em > adof< / em > value = dof_per_atom
dof_per_atom = define this many degrees-of-freedom per atom
< em > cdof< / em > value = dof_per_chunk
dof_per_chunk = define this many degrees-of-freedom per chunk
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > 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 > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > 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
center-of-mass velocity of each chunk. By specifying optional values,
it can also calulate the per-chunk temperature or energies of the
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multiple chunks of atoms.< / p >
< p > In LAMMPS, chunks are collections of atoms defined by a < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command, which assigns each atom
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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
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molecule or atoms in a spatial bin. See the < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > doc page and “ < a class = "reference internal" href = "Section_howto.html#howto-23" > < span > Section_howto 23< / span > < / a > 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.< / p >
< p > The temperature is calculated by the formula KE = DOF/2 k T, where KE =
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total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
v^2), DOF = the total number of degrees of freedom for those atoms, k
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= Boltzmann constant, and T = temperature.< / p >
< p > 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
cdof = degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the < a class = "reference internal" href = "dimension.html" > < em > dimension< / em > < / a >
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command, and cdof = 0.0. This gives the usual formula for
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temperature.< / p >
< p > 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
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.< / p >
< p > 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
the atoms may be dynamically assigned to chunks. Thus there is no
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need to use the < em > dynamic< / em > option of the
< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command for this compute style.< / p >
< p > If any optional values are specified, then per-chunk quantities are
also calculated and stored in a global array, as described below.< / p >
< p > The < em > temp< / em > 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
of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of
freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.< / p >
< p > 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 =
degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the < a class = "reference internal" href = "dimension.html" > < em > dimension< / em > < / a >
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command, and cdof = 0.0. This gives the usual formula for
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temperature.< / p >
< p > The < em > kecom< / em > 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.< / p >
< p > The < em > internal< / em > 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
the center-of-mass velocity of the chunk.< / p >
< hr class = "docutils" / >
< p > 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
atom. No rotational degrees of freedom are included for finite-size
particles. Also no degrees of freedom are subtracted for any velocity
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bias or constraints that are applied, such as < a class = "reference internal" href = "compute_temp_partial.html" > < em > compute temp/partial< / em > < / a > , or < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a >
or < a class = "reference internal" href = "fix_rigid.html" > < em > fix rigid< / em > < / a > . This is because those degrees of
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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
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< em > adof< / em > and < em > cdof< / em > keywords to adjust the calculated degress of freedom
appropriately, as explained below.< / p >
< p > Note that the per-chunk temperature calulated by this compute and the
< a class = "reference internal" href = "fix_ave_chunk.html" > < em > fix ave/chunk temp< / em > < / a > command can be different.
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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
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calculating the temperature; fix ave/chunk does not.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > Only atoms in the specified group contribute to the calculations
performed by this compute. The < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command defines its own group;
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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
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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.< / p >
< / div >
< p > The simplest way to output the per-chunk results of the compute
temp/chunk calculation to a file is to use the < a class = "reference internal" href = "fix_ave_time.html" > < em > fix ave/time< / em > < / a > command, for example:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > 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 > < / div >
< / div >
< hr class = "docutils" / >
< p > The keyword/value option pairs are used in the following ways.< / p >
< p > The < em > com< / em > keyword can be used with a value of < em > yes< / em > 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
temperature. This can be useful if the atoms are streaming or
otherwise moving collectively, and you wish to calculate only the
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thermal temperature.< / p >
< p > For the < em > bias< / em > keyword, < em > bias-ID< / em > refers to the ID of a temperature
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
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
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of the other per-chunk values, such as < em > kecom< / em > or < em > internal< / em > , which
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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,
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not on a per-chunk basis.< / p >
< p > The < em > adof< / em > and < em > cdof< / em > keywords define the values used in the degree of
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freedom (DOF) formulas used for the global or per-chunk temperature,
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:< / p >
< p > If spatially binned chunks contain some number of water molecules and
< a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > 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 < em > adof< / em > to 2.0.< / p >
< p > If < a class = "reference internal" href = "compute_temp_partial.html" > < em > compute temp/partial< / em > < / a > is used with the
< em > bias< / em > keyword to only allow the x component of velocity to contribute
to the temperature, then < em > adof< / em > = 1.0 would be appropriate.< / p >
< p > If each chunk consists of a large molecule, with some number of its
bonds constrained by < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > or the entire molecule
by < a class = "reference internal" href = "fix_rigid.html" > < em > fix rigid/small< / em > < / a > , < em > adof< / em > = 0.0 and < em > cdof< / em > could be
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set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
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molecule.< / p >
< hr class = "docutils" / >
< p > < strong > Output info:< / strong > < / p >
< p > 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.
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 < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > this section< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > 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 < em > Nchunk< / em > as calculated by the specified
< a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command. The number of
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columns is the number of specifed values (1 or more). These values
can be accessed by any command that uses global array values from a
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compute as input. Again, see < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > Section_howto 15< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > The scalar value calculated by this compute is “ intensive” . The
vector values are “ extensive” . The array values are “ intensive” .< / p >
< p > The scalar value will be in temperature < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > . The
vector values will be in energy < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > . The array values
will be in temperature < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > for the < em > temp< / em > value, and in
energy < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > for the < em > kecom< / em > and < em > internal< / em > values.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The < em > com< / em > and < em > bias< / em > keywords cannot be used together.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "compute_temp.html" > < em > compute temp< / em > < / a > , < a class = "reference internal" href = "fix_ave_chunk.html" > < em > fix ave/chunk temp< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are com no, no bias, adof = dimensionality of the
system (2 or 3), and cdof = 0.0.< / p >
< / div >
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