forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11607 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
0c22e8696a
commit
ac6f5afc2e
|
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@ -403,9 +403,9 @@ of each style or click on the style itself for a full description:
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|||
<TR ALIGN="center"><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
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</TD></TR></TABLE></DIV>
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<P>These are fix styles contributed by users, which can be used if
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|
|
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@ -539,6 +539,7 @@ of each style or click on the style itself for a full description:
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"store/force"_fix_store_force.html,
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"store/state"_fix_store_state.html,
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"temp/berendsen"_fix_temp_berendsen.html,
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"temp/csvr"_fix_temp_csvr.html,
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"temp/rescale"_fix_temp_rescale.html,
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"thermal/conductivity"_fix_thermal_conductivity.html,
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"tmd"_fix_tmd.html,
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|
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@ -1613,16 +1613,17 @@ velocity of spherical or aspherical particles to be adjusted in
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prescribed ways.
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</P>
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<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
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case by a pair style. Four thermostatting fixes are currently
|
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available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
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rescaling (temp/rescale). Dissipative particle dynamics (DPD)
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thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
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case by a pair style. Several thermostatting fixes are available:
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Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
|
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(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
|
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can be invoked via the <I>dpd/tstat</I> pair style:
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</P>
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<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
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<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
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<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
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<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
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<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
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<LI><A HREF = "fix_temp_csvr.html">fix temp/csvr</A>
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<LI><A HREF = "fix_langevin.html">fix langevin</A>
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<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
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<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
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|
|
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@ -1600,16 +1600,17 @@ velocity of spherical or aspherical particles to be adjusted in
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prescribed ways.
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Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
|
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case by a pair style. Four thermostatting fixes are currently
|
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available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
|
||||
rescaling (temp/rescale). Dissipative particle dynamics (DPD)
|
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thermostatting can be invoked via the {dpd/tstat} pair style:
|
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case by a pair style. Several thermostatting fixes are available:
|
||||
Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
|
||||
(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
|
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can be invoked via the {dpd/tstat} pair style:
|
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"fix nvt"_fix_nh.html
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"fix nvt/sphere"_fix_nvt_sphere.html
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"fix nvt/asphere"_fix_nvt_asphere.html
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"fix nvt/sllod"_fix_nvt_sllod.html
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"fix temp/berendsen"_fix_temp_berendsen.html
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"fix temp/csvr"_fix_temp_csvr.html
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"fix langevin"_fix_langevin.html
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"fix temp/rescale"_fix_temp_rescale.html
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"pair_style dpd/tstat"_pair_dpd.html :ul
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|
|
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@ -0,0 +1,161 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix temp/csvr command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>temp/csvr = style name of this fix command
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<LI>Tstart,Tstop = desired temperature at start/end of run
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<PRE> Tstart can be a variable (see below)
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</PRE>
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<LI>Tdamp = temperature damping parameter (time units)
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<LI>seed = random number seed to use for white noise (positive integer)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all temp/csvr 300.0 300.0 100.0 54324
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Adjust the temperature with a CSVR thermostat <A HREF = "#Bussi">(Bussi)</A>, which
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updates the velocities to a linear combination of the current
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velocities with a gaussian distribution at the desired temperature in
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every timestep.
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</P>
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<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
|
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particles which have rotational degrees of freedom are being
|
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thermostatted with this fix. The translational degrees of freedom can
|
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also have a bias velocity removed from them before thermostatting
|
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takes place; see the description below.
|
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</P>
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<P>The desired temperature at each timestep is a ramped value during the
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run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
|
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time units and determines how rapidly the temperature is relaxed. For
|
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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 HREF = "units.html">units</A> command).
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</P>
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<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
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In this case, the <I>Tstop</I> 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
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name. In this case, the variable will be evaluated each timestep, and
|
||||
its value used to determine the target temperature.
|
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</P>
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<P>Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent temperature.
|
||||
</P>
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||||
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</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, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
|
||||
atoms 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 HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
|
||||
langevin</A> commands.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
thermostatting.
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||||
</P>
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||||
<P>This fix computes a temperature each timestep. To do this, the fix
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||||
creates its own compute of style "temp", as if this command had been
|
||||
issued:
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||||
</P>
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||||
<PRE>compute fix-ID_temp group-ID temp
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</PRE>
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||||
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
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that the ID of the new compute is the fix-ID + underscore + "temp",
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||||
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
|
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the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
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||||
This means you can change the attributes of this fix's temperature
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||||
(e.g. its degrees-of-freedom) via the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
|
||||
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
|
||||
custom</A> command using the appropriate compute-ID.
|
||||
It also means that changing attributes of <I>thermo_temp</I> will have no
|
||||
effect on this fix.
|
||||
</P>
|
||||
<P>Like other fixes that perform thermostatting, this fix can be used
|
||||
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
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||||
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 HREF = "fix_modify.html">fix_modify</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 HREF = "compute.html">compute
|
||||
commands</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>
|
||||
<HR>
|
||||
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>.
|
||||
</P>
|
||||
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
|
||||
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</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 HREF = "fix_modify.html">fix_modify</A> <I>energy</I> 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 HREF = "thermo_style.html">thermodynamic
|
||||
output</A>.
|
||||
</P>
|
||||
<P>This fix computes a global scalar which can be accessed by various
|
||||
<A HREF = "Section_howto.html#howto_15">output commands</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
|
||||
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
|
||||
<A HREF = "run.html">run</A> command for details of how to do this.
|
||||
</P>
|
||||
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
|
||||
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
|
||||
<A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
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|
||||
<A NAME = "Bussi"></A>
|
||||
|
||||
<P><B>(Bussi)</B> Bussi and Parrinello, Phys. Rev. E (2007)
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,151 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix temp/csvr command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID temp/csvr Tstart Tstop Tdamp seed :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
temp/csvr = style name of this fix command :l
|
||||
Tstart,Tstop = desired temperature at start/end of run :l
|
||||
Tstart can be a variable (see below) :pre
|
||||
Tdamp = temperature damping parameter (time units) :l
|
||||
seed = random number seed to use for white noise (positive integer) :l,ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all temp/csvr 300.0 300.0 100.0 54324 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Adjust the temperature with a CSVR thermostat "(Bussi)"_#Bussi, which
|
||||
updates the velocities to a linear combination of the current
|
||||
velocities with a gaussian distribution at the desired temperature in
|
||||
every timestep.
|
||||
|
||||
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.
|
||||
|
||||
The desired temperature at each timestep is a ramped value during the
|
||||
run from {Tstart} to {Tstop}. The {Tdamp} 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
|
||||
"units"_units.html command).
|
||||
|
||||
{Tstart} can be specified as an equal-style "variable"_variable.html.
|
||||
In this case, the {Tstop} 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.
|
||||
|
||||
Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include "thermo_style"_thermo_style.html command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent temperature.
|
||||
|
||||
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html 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, like "fix nve"_fix_nve.html to actually update the positions of
|
||||
atoms 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 "fix nvt"_fix_nh.html or "fix
|
||||
langevin"_fix_langevin.html commands.
|
||||
|
||||
See "this howto section"_Section_howto.html#howto_16 of the manual for
|
||||
a discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
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:
|
||||
|
||||
compute fix-ID_temp group-ID temp :pre
|
||||
|
||||
See the "compute temp"_compute_temp.html 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.
|
||||
|
||||
Note that this is NOT the compute used by thermodynamic output (see
|
||||
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
|
||||
This means you can change the attributes of this fix's temperature
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
"compute_modify"_compute_modify.html command or print this temperature
|
||||
during thermodynamic output via the "thermo_style
|
||||
custom"_thermo_style.html command using the appropriate compute-ID.
|
||||
It also means that changing attributes of {thermo_temp} will have no
|
||||
effect on this fix.
|
||||
|
||||
Like other fixes that perform thermostatting, this fix can be used
|
||||
with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
|
||||
to assign a temperature compute to this fix that includes such a bias
|
||||
term. See the doc pages for individual "compute
|
||||
commands"_compute.html 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.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {temp} option is supported by this
|
||||
fix. You can use it to assign a temperature "compute"_compute.html
|
||||
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.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} 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 "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
cummulative energy change due to this fix. The scalar value
|
||||
calculated by this fix is "extensive".
|
||||
|
||||
This fix can ramp its target temperature over multiple runs, using the
|
||||
{start} and {stop} keywords of the "run"_run.html command. See the
|
||||
"run"_run.html command for details of how to do this.
|
||||
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
|
||||
"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html,
|
||||
"fix temp/berendsen"_fix_temp_berendsen.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Bussi)
|
||||
|
||||
[(Bussi)] Bussi and Parrinello, Phys. Rev. E (2007)
|
||||
Loading…
Reference in New Issue