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2015-07-30 22:53:28 +08:00
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< title > compute temp/rotate command — LAMMPS 15 May 2015 version documentation< / title >
2011-08-09 05:22:57 +08:00
2015-07-30 22:53:28 +08:00
2011-08-09 05:22:57 +08:00
2015-07-30 22:53:28 +08:00
2011-08-09 05:22:57 +08:00
2015-07-30 22:53:28 +08:00
2011-08-09 05:22:57 +08:00
2015-07-30 22:53:28 +08:00
2011-08-09 05:22:57 +08:00
2015-07-30 22:53:28 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
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< li > compute temp/rotate command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > compute temp/rotate command< a class = "headerlink" href = "#compute-temp-rotate-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/rotate
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< 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/rotate = style name of this compute command< / li >
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< 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 Tbead bead temp/rotate
< / pre > < / div >
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< 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, after subtracting out the center-of-mass velocity and angular velocity of the group.
This is useful if the group is expected to have a non-zero net
velocity and/or global rotation motion for some reason. A compute of this style can be used by any
command that computes a temperature,
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e.g. < a class = "reference internal" href = "thermo_modify.html" > < em > thermo_modify< / em > < / a > , < a class = "reference internal" href = "fix_temp_rescale.html" > < em > fix temp/rescale< / em > < / a > , < a class = "reference internal" href = "fix_nh.html" > < em > fix npt< / em > < / a > , etc.< / p >
< p > After the center-of-mass velocity and angular velocity has been subtracted from each atom,
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the temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in the group, k = Boltzmann constant, and T = 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 > The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the < em > dynamic< / em > option of the
< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command if this is not the case.< / p >
< p > The removal of the center-of-mass velocity and angular velocity by this fix is essentially
computing the temperature after a “ bias” has been removed from the
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velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
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that work in this way include < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > , < a class = "reference internal" href = "fix_temp_rescale.html" > < em > fix temp/rescale< / em > < / a > , < a class = "reference internal" href = "fix_temp_berendsen.html" > < em > fix temp/berendsen< / em > < / a > , and < a class = "reference internal" href = "fix_langevin.html" > < em > fix langevin< / em > < / a > .< / p >
< p > This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > and
< a class = "reference internal" href = "fix_rigid.html" > < em > fix rigid< / em > < / a > . This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
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< em > extra< / em > option of the < a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command.< / p >
< p > See < a class = "reference internal" href = "Section_howto.html#howto-16" > < span > this howto section< / span > < / a > of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.< / p >
< 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 > The scalar value calculated by this compute is “ intensive” . The
vector values are “ extensive” .< / 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 > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This compute is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / 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 > < / p >
< p > < strong > Default:< / strong > none< / p >
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