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< li > fix temp/csvr command< / li >
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< div class = "section" id = "fix-temp-csvr-command" >
< span id = "index-0" > < / span > < h1 > fix temp/csvr command< a class = "headerlink" href = "#fix-temp-csvr-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "fix-temp-csld-command" >
< h1 > fix temp/csld command< a class = "headerlink" href = "#fix-temp-csld-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 > fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID temp/csld Tstart Tstop Tdamp seed
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > temp/csvr or temp/csld = style name of this fix command< / li >
< li > Tstart,Tstop = desired temperature at start/end of run< / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > Tstart can be a variable (see below)
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > Tdamp = temperature damping parameter (time units)< / li >
< li > seed = random number seed to use for white noise (positive integer)< / li >
< / ul >
< / 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 > fix 1 all temp/csvr 300.0 300.0 100.0 54324
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 1 all temp/csld 100.0 300.0 10.0 123321
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Adjust the temperature with a canonical sampling thermostat that uses
global velocity rescaling with Hamiltonian dynamics (< em > temp/csvr< / em > )
< a class = "reference internal" href = "#bussi1" > < span > (Bussi1)< / span > < / a > , or Langevin dynamics (< em > temp/csld< / em > )
< a class = "reference internal" href = "#bussi2" > < span > (Bussi2)< / span > < / a > . In the case of < em > temp/csvr< / em > the thermostat is
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similar to the empirical Berendsen thermostat in
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< a class = "reference internal" href = "fix_temp_berendsen.html" > < em > temp/berendsen< / em > < / a > , but chooses the actual
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scaling factor from a suitably chosen (gaussian) distribution rather
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than having it determined from the time constant directly. In the case
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of < em > temp/csld< / em > the velocities are updated to a linear combination of
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the current velocities with a gaussian distribution of velocities at
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the desired temperature. Both termostats are applied every timestep.< / p >
< p > The thermostat is applied to only the translational degrees of freedom
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for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
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thermostatted with these fixes. The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
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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
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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" > < em > units< / em > < / a > command).< / p >
< p > < em > Tstart< / em > can be specified as an equal-style < a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > .
In this case, the < em > Tstop< / em > setting is ignored. If the value is a
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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
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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" > < em > thermo_style< / em > < / a > command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Unlike the < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > command which
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performs Nose/Hoover thermostatting AND time integration, these fixes
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do NOT perform time integration. They only modify 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" > < em > fix nve< / em > < / a > to actually update the positions of atoms
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using the modified velocities. Likewise, these fixes should not
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normally be used on atoms that also have their temperature controlled
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by another fix - e.g. by < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > or < a class = "reference internal" href = "fix_langevin.html" > < em > fix langevin< / em > < / a > commands.< / p >
< / div >
< 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 > These fixes compute 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-python" > < div class = "highlight" > < pre > compute fix-ID_temp group-ID temp
< / pre > < / div >
< / div >
< p > See the < a class = "reference internal" href = "compute_temp.html" > < em > compute temp< / em > < / 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" > < em > thermo_style< / em > < / a > command) with ID = < em > thermo_temp< / em > .
This means you can change the attributes of this fix’ s temperature
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(e.g. its degrees-of-freedom) via the
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< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command or print this temperature
during thermodynamic output via the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / 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, these fixes can be used
with < a class = "reference internal" href = "compute.html" > < em > compute commands< / em > < / a > that calculate a temperature
after removing a “ bias” from the atom velocities. E.g. removing the
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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
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default, but only if the < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual < a class = "reference internal" href = "compute.html" > < em > compute commands< / em > < / a > to determine which ones include a bias. In
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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
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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< a class = "headerlink" href = "#restart-fix-modify-output-run-start-stop-minimize-info" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > No information about these fixes are written to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > .< / p >
< p > The < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > < em > temp< / em > option is supported by these
fixes. You can use it to assign a temperature < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a >
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you have defined to these fixes which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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these fixes and by the compute should be the same.< / p >
< p > These fixes 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" > < em > run< / em > < / a > command. See the
< a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command for details of how to do this.< / p >
< p > These fixes are not invoked during < a class = "reference internal" href = "minimize.html" > < em > energy minimization< / em > < / a > .< / p >
< p > These fixes compute a global scalar which can be accessed by various
< a class = "reference internal" href = "Section_howto.html#howto-15" > < span > output commands< / span > < / a > . The scalar is the
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cummulative energy change due to the fix. The scalar value
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calculated by this fix is “ extensive” .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > These fixes are not compatible with < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > .< / p >
< p > The fix can be used with dynamic groups as defined by the
< a class = "reference internal" href = "group.html" > < em > group< / em > < / a > command. Likewise it can be used with groups to
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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
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over time or the atom count becomes very small.< / 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 = "fix_nve.html" > < em > fix nve< / em > < / a > , < 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_langevin.html" > < em > fix langevin< / em > < / a > ,
< a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > , < a class = "reference internal" href = "compute_temp.html" > < em > compute temp< / em > < / a > ,
< a class = "reference internal" href = "fix_temp_berendsen.html" > < em > fix temp/berendsen< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "bussi2" > < span id = "bussi1" > < / span > < strong > (Bussi1)< / strong > Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)< / p >
< p > < strong > (Bussi2)< / strong > Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)< / p >
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