2016-05-10 01:33:12 +08:00
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< li > fix temp/berendsen command< / li >
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< div class = "section" id = "fix-temp-berendsen-command" >
< span id = "index-0" > < / span > < h1 > fix temp/berendsen command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > temp< / span > < span class = "o" > /< / span > < span class = "n" > berendsen< / span > < span class = "n" > Tstart< / span > < span class = "n" > Tstop< / span > < span class = "n" > Tdamp< / span >
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < span class = "doc" > fix< / span > < / a > command< / li >
< li > temp/berendsen = style name of this fix command< / li >
< li > Tstart,Tstop = desired temperature at start/end of run< / li >
< / ul >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > Tstart< / span > < span class = "n" > can< / span > < span class = "n" > be< / span > < span class = "n" > a< / span > < span class = "n" > variable< / span > < span class = "p" > (< / span > < span class = "n" > see< / span > < span class = "n" > below< / span > < span class = "p" > )< / span >
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > Tdamp = temperature damping parameter (time units)< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "mi" > 1< / span > < span class = "nb" > all< / span > < span class = "n" > temp< / span > < span class = "o" > /< / span > < span class = "n" > berendsen< / span > < span class = "mf" > 300.0< / span > < span class = "mf" > 300.0< / span > < span class = "mf" > 100.0< / span >
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Reset the temperature of a group of atoms by using a Berendsen
thermostat < a class = "reference internal" href = "#berendsen" > < span class = "std std-ref" > (Berendsen)< / span > < / a > , which rescales their velocities
every timestep.< / p >
< p > The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
takes place; see the description below.< / p >
< p > The desired temperature at each timestep is a ramped value during the
run from < em > Tstart< / em > to < em > Tstop< / em > . The < em > Tdamp< / em > parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
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< a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > command).< / p >
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< p > < em > Tstart< / em > can be specified as an equal-style < a class = "reference internal" href = "variable.html" > < span class = "doc" > variable< / span > < / a > .
In this case, the < em > Tstop< / em > setting is ignored. If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the target temperature.< / p >
< p > Equal-style variables can specify formulas with various mathematical
functions, and include < a class = "reference internal" href = "thermo_style.html" > < span class = "doc" > thermo_style< / span > < / a > command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.< / p >
< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > Unlike the < a class = "reference internal" href = "fix_nh.html" > < span class = "doc" > fix nvt< / span > < / a > command which performs
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies velocities to effect
thermostatting. Thus you must use a separate time integration fix,
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like < a class = "reference internal" href = "fix_nve.html" > < span class = "doc" > fix nve< / span > < / a > to actually update the positions of atoms
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using the modified velocities. Likewise, this fix should not normally
be used on atoms that also have their temperature controlled by
another fix - e.g. by < a class = "reference internal" href = "fix_nh.html" > < span class = "doc" > fix nvt< / span > < / a > or < a class = "reference internal" href = "fix_langevin.html" > < span class = "doc" > fix langevin< / span > < / a > commands.< / p >
< / div >
< p > See < a class = "reference internal" href = "Section_howto.html#howto-16" > < span class = "std std-ref" > this howto section< / span > < / a > of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.< / p >
< p > This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “ temp” , as if this command had been
issued:< / p >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "n" > fix< / span > < span class = "o" > -< / span > < span class = "n" > ID_temp< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > temp< / span >
< / pre > < / div >
< / div >
< p > See the < a class = "reference internal" href = "compute_temp.html" > < span class = "doc" > compute temp< / span > < / a > command for details. Note
that the ID of the new compute is the fix-ID + underscore + “ temp” ,
and the group for the new compute is the same as the fix group.< / p >
< p > Note that this is NOT the compute used by thermodynamic output (see
the < a class = "reference internal" href = "thermo_style.html" > < span class = "doc" > thermo_style< / span > < / a > command) with ID = < em > thermo_temp< / em > .
This means you can change the attributes of this fix’ s temperature
(e.g. its degrees-of-freedom) via the
< a class = "reference internal" href = "compute_modify.html" > < span class = "doc" > compute_modify< / span > < / a > command or print this temperature
during thermodynamic output via the < a class = "reference internal" href = "thermo_style.html" > < span class = "doc" > thermo_style custom< / span > < / a > command using the appropriate compute-ID.
It also means that changing attributes of < em > thermo_temp< / em > will have no
effect on this fix.< / p >
< p > Like other fixes that perform thermostatting, this fix can be used
with < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute commands< / span > < / a > that calculate a temperature
after removing a “ bias” from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute commands< / span > < / a > to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< / h2 >
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < span class = "doc" > binary restart files< / span > < / a > .< / p >
< p > The < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > < em > temp< / em > option is supported by this
fix. You can use it to assign a temperature < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute< / span > < / a >
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.< / p >
< p > The < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > < em > energy< / em > option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system’ s potential energy as part of < a class = "reference internal" href = "thermo_style.html" > < span class = "doc" > thermodynamic output< / span > < / a > .< / p >
< p > This fix computes a global scalar which can be accessed by various
< a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > output commands< / span > < / a > . The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is “ extensive” .< / p >
< p > This fix can ramp its target temperature over multiple runs, using the
< em > start< / em > and < em > stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < span class = "doc" > run< / span > < / a > command. See the
< a class = "reference internal" href = "run.html" > < span class = "doc" > run< / span > < / a > command for details of how to do this.< / p >
< p > This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < span class = "doc" > energy minimization< / span > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< p > This fix can be used with dynamic groups as defined by the
< a class = "reference internal" href = "group.html" > < span class = "doc" > group< / span > < / a > command. Likewise it can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
over time or the atom count becomes very small.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
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< p > < a class = "reference internal" href = "fix_nve.html" > < span class = "doc" > fix nve< / span > < / a > , < a class = "reference internal" href = "fix_nh.html" > < span class = "doc" > fix nvt< / span > < / a > , < a class = "reference internal" href = "fix_temp_rescale.html" > < span class = "doc" > fix temp/rescale< / span > < / a > , < a class = "reference internal" href = "fix_langevin.html" > < span class = "doc" > fix langevin< / span > < / a > ,
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< a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > , < a class = "reference internal" href = "compute_temp.html" > < span class = "doc" > compute temp< / span > < / a > ,
< a class = "reference internal" href = "fix_press_berendsen.html" > < span class = "doc" > fix press/berendsen< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "berendsen" > < strong > (Berendsen)< / strong > Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).< / p >
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