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@ -1019,78 +1019,137 @@ frequencies and global vs per-atom attributes are the same.
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<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
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<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
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</H4>
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</H4>
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<P> add a HowTo on time integration options and/or thermostat/temperature options
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<P>Thermostatting means controlling the temperature of particles in an MD
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4 thermostats
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simulation. Barostatting means controlling the pressure. Since the
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which do integration, which need fix nve or fix nph
|
pressure includes a kinetic component due to particle velocities, both
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all can be used with press/berendsen
|
these operations require calculation of the temperature. Typically a
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only NVT thermostats rotational degrees of freedom directly
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target temperature (T) and/or pressure (P) is specified by the user,
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what bias is, how to remove it
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and the thermostat or barostat attempts to equilibrate the system to
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howto remove bias for temp/sphere and temp/asphere
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the requested T and/or P.
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which biases can be doubled up via compute_modify bias command
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</P>
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</P>
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<P>Enhanced the computes that calculate temperature, thermostatting
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<P>Temperature is computed as kinetic energy divided by some number of
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fixes, and time integrators that use temperature control to be more
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degrees of freedom (and the Boltzmann constant). Since kinetic energy
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flexible and consistent. This is for point particles, extended
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is a function of particle velocity, there is often a need to
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spherical particles, and <A HREF = "doc/Section_howto.html#4_14">aspherical
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distinguish between a particle's advection velocity (due to some
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particles</A>. Also Added new <A HREF = "doc/compute_ke.html">compute
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aggregate motiion of particles) and its thermal velocity. The sum of
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ke</A> and <A HREF = "doc/compute_erotate_asphere.html">compute
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the two is the particle's total velocity, but the latter is often what
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erotate/asphere</A> commands.
|
is wanted to compute a temperature.
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</P>
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</P>
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<P>These <A HREF = "doc/compute.html">compute commands</A> calculate temperature. All
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<P>LAMMPS has several options for computing temperatures and for using
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but the first 3 calculate velocity biases that are removed when
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them in thermostatting and barostatting.
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computing a temperature. Temp/sphere and temp/asphere now allow
|
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computes that calculate such a biased temperature to be included as an
|
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additional argument, so that the translational velocity of extended
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spherical or aspherical particles can also be altered in prescribed
|
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ways.
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</P>
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</P>
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<UL><LI><A HREF = "doc/compute_temp.html">compute temp</A>
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<P>These <A HREF = "compute.html">compute commands</A> calculate temperature.
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<LI><A HREF = "doc/compute_temp_sphere.html">compute temp/sphere</A>
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</P>
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<LI><A HREF = "doc/compute_temp_asphere.html">compute temp/asphere</A>
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<UL><LI><A HREF = "compute_temp.html">compute temp</A>
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<LI><A HREF = "doc/compute_temp_com.html">compute temp/com</A>
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<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
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<LI><A HREF = "doc/compute_temp_deform.html">compute temp/deform</A>
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<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
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<LI><A HREF = "doc/compute_temp_partial.html">compute temp/partial</A>
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<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
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<LI><A HREF = "doc/compute_temp_ramp.html">compute temp/ramp</A>
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<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
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<LI><A HREF = "doc/compute_temp_region.html">compute temp/region</A>
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<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
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<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
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<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
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</UL>
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</UL>
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<P>Four thermostatting methods are available: Nose-Hoover, Berendsen,
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<P>All but the first 3 calculate velocity biases (i.e. advection
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Langevin, and direct rescaling. Nose/Hoover works on rotational
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velocities) that are removed when computing the thermal temperature.
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degrees-of-freedom for spherical and aspherical particles; the others
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<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
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only work on translational degrees of freedom. Any of these methods
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temp/asphere</A> compute kinetic energy for
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can use temperature computes that remove bias for the purpose of
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extended particles that includes rotational degrees of freedom. They
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computing the current temperature and performing thermostatting only
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both allow, as an extra argument, another temperature compute that
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on the remaining thermal velocity. For <A HREF = "doc/Section_howto.html#4_13">non-equilibrium MD
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subtracts a velocity bias, so the translational velocity of extended
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simulations</A>., there is also a SLLOD fix
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spherical or aspherical particles can be adjusted in prescribed ways.
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which does NVT thermostatting in conjunction with the SLLOD equations
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of motion. These are the relevant <A HREF = "doc/fix.html">fix commands</A>:
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</P>
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</P>
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<UL><LI><A HREF = "doc/fix_nvt.html">fix nvt</A>
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<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>. Four
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<LI><A HREF = "doc/fix_nvt_sphere.html">fix nvt/sphere</A>
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thermostatting fixes are currently available: Nose-Hoover (nvt),
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<LI><A HREF = "doc/fix_nvt_asphere.html">fix nvt/asphere</A>
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Berendsen, Langevin, and direct rescaling (temp/rescale):
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<LI><A HREF = "doc/fix_nvt_sllod.html">fix nvt/sllod</A>
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</P>
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<LI><A HREF = "doc/fix_temp_berendsen.html">fix temp/berendsen</A>
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<UL><LI><A HREF = "fix_nvt.html">fix nvt</A>
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<LI><A HREF = "doc/fix_langevin.html">fix langevin</A>
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<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
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<LI><A HREF = "doc/fix_temp_rescale.html">fix temp/rescale</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_langevin.html">fix langevin</A>
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<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
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</UL>
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</UL>
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<P>Note that only the nvt fixes perform time integration. The others
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<P><A HREF = "fix_nvt.html">Fix nvt</A> only thermostats the translational velocity of
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should be used with an NVE integration fix such as these:
|
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> does as well, except
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that it subtracts out a velocity bias due to a deforming box and
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integrates the SLLOD equations of motion. See the <A HREF = "#4_13">NEMD
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simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
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nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
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nvt/asphere</A> thermostat not only translation
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velocities but also rotational velocities for spherical and aspherical
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particles.
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</P>
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</P>
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<UL><LI><A HREF = "doc/fix_nve.html">fix nve</A>
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<P>Any of these fixes can use temperature computes that remove bias for
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<LI><A HREF = "doc/fix_nve_sphere.html">fix nve/sphere</A>
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two purposes: (a) computing the current temperature to compare to the
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requested target temperature, and (b) adjusting only the thermal
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temperature component of the particle's velocities. See the doc pages
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for the individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A>
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command for instructions on how to assign a temperature compute to a
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thermostatting fix.
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</P>
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<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
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they update the velocities and positions of particles due to forces
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and velocities respectively. The other thermostat fixes only adjust
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velocities; they do NOT perform time integration. Thus they should be
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used in conjunction with a constant NVE integration fix such as these:
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</P>
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<UL><LI><A HREF = "fix_nve.html">fix nve</A>
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<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
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<LI><A HREF = "doc_fix_nve_asphere.html">fix nve/asphere</A>
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<LI><A HREF = "doc_fix_nve_asphere.html">fix nve/asphere</A>
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</UL>
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</UL>
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<P>Two barosttating methods are available: Nose-Hoover and Berendsen.
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<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
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The fix npt commands include Nose-Hoover thermostatting. Fix nph and
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barosttating methods are currently available: Nose-Hoover (npt and
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fix press/bernendsen can be used in conjunction with any of the 4
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nph) and Berendsen:
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thermostatting methods. These are the relevant <A HREF = "doc/fix.html">fix
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commands</A>:
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</P>
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</P>
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<UL><LI><A HREF = "doc/fix_npt.html">fix npt</A>
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<UL><LI><A HREF = "fix_npt.html">fix npt</A>
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<LI><A HREF = "doc/fix_npt_sphere.html">fix npt/sphere</A>
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<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
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<LI><A HREF = "doc/fix_npt_asphere.html">fix npt/asphere</A>
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<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
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<LI><A HREF = "doc/fix_nph.html">fix nph</A>
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<LI><A HREF = "fix_nph.html">fix nph</A>
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<LI><A HREF = "doc/fix_press_berendsen.html">fix press/berendsen</A>
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<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
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</UL>
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</UL>
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<P>The <A HREF = "fix_npt.html">fix npt</A> commands include a Nose-Hoover thermostat
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and barostat. <A HREF = "fix_nph.html">Fix nph</A> is just a Nose/Hoover barostat;
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it does no thermostatting. Both <A HREF = "fix_nph.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
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press/bernendsen</A> can be used in conjunction
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with any of the thermostatting fixes.
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</P>
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<P>As with the thermostats, <A HREF = "fix_npt.html">fix npt</A> and <A HREF = "fix_nph.html">fix
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nph</A> only use translational motion of the particles in
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|
computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
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npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
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npt/asphere</A> thermo/barostat using not only
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translation velocities but also rotational velocities for spherical
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and aspherical particles.
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</P>
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<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
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|
pressure</A> compute to calculate a current
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|
pressure. The barostatting fixes can also use temperature computes
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|
that remove bias for the purpose of computing the current temperature
|
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|
which contributes to the current pressure. See the doc pages for the
|
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|
individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A> command for
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|
instructions on how to assign a temperature or pressure compute to a
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|
barostatting fix.
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</P>
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<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_npt.html">fix
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npt</A> and <A HREF = "fix_nph.html">fix nph</A>) perform time
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|
integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
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|
so it should be used with one of the constant NVE fixes or with one of
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|
the NVT fixes.
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</P>
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|
<P>Finally, thermodynamic output, which can be setup via the
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<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
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and pressure values. As explained on the doc page for the
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<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
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setup by the thermo command itself. They are NOT the ones associated
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with any thermostatting or barostatting fix you have defined or with
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any compute that calculates a temperature or pressure. Thus if you
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want to view these values of T and P, you need to specify them
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explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
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you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
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re-define what temperature or pressure compute is used for default
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thermodynamic output.
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</P>
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<HR>
|
<HR>
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|
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<HR>
|
<HR>
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|
|
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|
|
@ -1010,79 +1010,136 @@ run every: any variable: nevery: screen, log: nevery :tb(s=:)
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4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
|
4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
|
||||||
|
|
||||||
add a HowTo on time integration options and/or thermostat/temperature options
|
Thermostatting means controlling the temperature of particles in an MD
|
||||||
4 thermostats
|
simulation. Barostatting means controlling the pressure. Since the
|
||||||
which do integration, which need fix nve or fix nph
|
pressure includes a kinetic component due to particle velocities, both
|
||||||
all can be used with press/berendsen
|
these operations require calculation of the temperature. Typically a
|
||||||
only NVT thermostats rotational degrees of freedom directly
|
target temperature (T) and/or pressure (P) is specified by the user,
|
||||||
what bias is, how to remove it
|
and the thermostat or barostat attempts to equilibrate the system to
|
||||||
howto remove bias for temp/sphere and temp/asphere
|
the requested T and/or P.
|
||||||
which biases can be doubled up via compute_modify bias command
|
|
||||||
|
|
||||||
Enhanced the computes that calculate temperature, thermostatting
|
Temperature is computed as kinetic energy divided by some number of
|
||||||
fixes, and time integrators that use temperature control to be more
|
degrees of freedom (and the Boltzmann constant). Since kinetic energy
|
||||||
flexible and consistent. This is for point particles, extended
|
is a function of particle velocity, there is often a need to
|
||||||
spherical particles, and "aspherical
|
distinguish between a particle's advection velocity (due to some
|
||||||
particles"_doc/Section_howto.html#4_14. Also Added new "compute
|
aggregate motiion of particles) and its thermal velocity. The sum of
|
||||||
ke"_doc/compute_ke.html and "compute
|
the two is the particle's total velocity, but the latter is often what
|
||||||
erotate/asphere"_doc/compute_erotate_asphere.html commands.
|
is wanted to compute a temperature.
|
||||||
|
|
||||||
These "compute commands"_doc/compute.html calculate temperature. All
|
LAMMPS has several options for computing temperatures and for using
|
||||||
but the first 3 calculate velocity biases that are removed when
|
them in thermostatting and barostatting.
|
||||||
computing a temperature. Temp/sphere and temp/asphere now allow
|
|
||||||
computes that calculate such a biased temperature to be included as an
|
|
||||||
additional argument, so that the translational velocity of extended
|
|
||||||
spherical or aspherical particles can also be altered in prescribed
|
|
||||||
ways.
|
|
||||||
|
|
||||||
"compute temp"_doc/compute_temp.html
|
These "compute commands"_compute.html calculate temperature.
|
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"compute temp/sphere"_doc/compute_temp_sphere.html
|
|
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"compute temp/asphere"_doc/compute_temp_asphere.html
|
|
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"compute temp/com"_doc/compute_temp_com.html
|
|
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"compute temp/deform"_doc/compute_temp_deform.html
|
|
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"compute temp/partial"_doc/compute_temp_partial.html
|
|
||||||
"compute temp/ramp"_doc/compute_temp_ramp.html
|
|
||||||
"compute temp/region"_doc/compute_temp_region.html :ul
|
|
||||||
|
|
||||||
Four thermostatting methods are available: Nose-Hoover, Berendsen,
|
"compute temp"_compute_temp.html
|
||||||
Langevin, and direct rescaling. Nose/Hoover works on rotational
|
"compute temp/sphere"_compute_temp_sphere.html
|
||||||
degrees-of-freedom for spherical and aspherical particles; the others
|
"compute temp/asphere"_compute_temp_asphere.html
|
||||||
only work on translational degrees of freedom. Any of these methods
|
"compute temp/com"_compute_temp_com.html
|
||||||
can use temperature computes that remove bias for the purpose of
|
"compute temp/deform"_compute_temp_deform.html
|
||||||
computing the current temperature and performing thermostatting only
|
"compute temp/partial"_compute_temp_partial.html
|
||||||
on the remaining thermal velocity. For "non-equilibrium MD
|
"compute temp/ramp"_compute_temp_ramp.html
|
||||||
simulations"_doc/Section_howto.html#4_13., there is also a SLLOD fix
|
"compute temp/region"_compute_temp_region.html :ul
|
||||||
which does NVT thermostatting in conjunction with the SLLOD equations
|
|
||||||
of motion. These are the relevant "fix commands"_doc/fix.html:
|
|
||||||
|
|
||||||
"fix nvt"_doc/fix_nvt.html
|
All but the first 3 calculate velocity biases (i.e. advection
|
||||||
"fix nvt/sphere"_doc/fix_nvt_sphere.html
|
velocities) that are removed when computing the thermal temperature.
|
||||||
"fix nvt/asphere"_doc/fix_nvt_asphere.html
|
"Fix temp/sphere"_fix_temp_sphere.html and "fix
|
||||||
"fix nvt/sllod"_doc/fix_nvt_sllod.html
|
temp/asphere"_fix_temp_asphere.html compute kinetic energy for
|
||||||
"fix temp/berendsen"_doc/fix_temp_berendsen.html
|
extended particles that includes rotational degrees of freedom. They
|
||||||
"fix langevin"_doc/fix_langevin.html
|
both allow, as an extra argument, another temperature compute that
|
||||||
"fix temp/rescale"_doc/fix_temp_rescale.html :ul
|
subtracts a velocity bias, so the translational velocity of extended
|
||||||
|
spherical or aspherical particles can be adjusted in prescribed ways.
|
||||||
|
|
||||||
Note that only the nvt fixes perform time integration. The others
|
Thermostatting in LAMMPS is performed by "fixes"_fix.html. Four
|
||||||
should be used with an NVE integration fix such as these:
|
thermostatting fixes are currently available: Nose-Hoover (nvt),
|
||||||
|
Berendsen, Langevin, and direct rescaling (temp/rescale):
|
||||||
|
|
||||||
"fix nve"_doc/fix_nve.html
|
"fix nvt"_fix_nvt.html
|
||||||
"fix nve/sphere"_doc/fix_nve_sphere.html
|
"fix nvt/sphere"_fix_nvt_sphere.html
|
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|
"fix nvt/asphere"_fix_nvt_asphere.html
|
||||||
|
"fix nvt/sllod"_fix_nvt_sllod.html
|
||||||
|
"fix temp/berendsen"_fix_temp_berendsen.html
|
||||||
|
"fix langevin"_fix_langevin.html
|
||||||
|
"fix temp/rescale"_fix_temp_rescale.html :ul
|
||||||
|
|
||||||
|
"Fix nvt"_fix_nvt.html only thermostats the translational velocity of
|
||||||
|
particles. "Fix nvt/sllod"_fix_nvt_sllod.html does as well, except
|
||||||
|
that it subtracts out a velocity bias due to a deforming box and
|
||||||
|
integrates the SLLOD equations of motion. See the "NEMD
|
||||||
|
simulations"_#4_13 section of this page for further details. "Fix
|
||||||
|
nvt/sphere"_fix_nvt_sphere.html and "fix
|
||||||
|
nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
|
||||||
|
velocities but also rotational velocities for spherical and aspherical
|
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|
particles.
|
||||||
|
|
||||||
|
Any of these fixes can use temperature computes that remove bias for
|
||||||
|
two purposes: (a) computing the current temperature to compare to the
|
||||||
|
requested target temperature, and (b) adjusting only the thermal
|
||||||
|
temperature component of the particle's velocities. See the doc pages
|
||||||
|
for the individual fixes and for the "fix_modify"_fix_modify.html
|
||||||
|
command for instructions on how to assign a temperature compute to a
|
||||||
|
thermostatting fix.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
|
||||||
|
they update the velocities and positions of particles due to forces
|
||||||
|
and velocities respectively. The other thermostat fixes only adjust
|
||||||
|
velocities; they do NOT perform time integration. Thus they should be
|
||||||
|
used in conjunction with a constant NVE integration fix such as these:
|
||||||
|
|
||||||
|
"fix nve"_fix_nve.html
|
||||||
|
"fix nve/sphere"_fix_nve_sphere.html
|
||||||
"fix nve/asphere"_doc_fix_nve_asphere.html :ul
|
"fix nve/asphere"_doc_fix_nve_asphere.html :ul
|
||||||
|
|
||||||
Two barosttating methods are available: Nose-Hoover and Berendsen.
|
Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two
|
||||||
The fix npt commands include Nose-Hoover thermostatting. Fix nph and
|
barosttating methods are currently available: Nose-Hoover (npt and
|
||||||
fix press/bernendsen can be used in conjunction with any of the 4
|
nph) and Berendsen:
|
||||||
thermostatting methods. These are the relevant "fix
|
|
||||||
commands"_doc/fix.html:
|
|
||||||
|
|
||||||
"fix npt"_doc/fix_npt.html
|
"fix npt"_fix_npt.html
|
||||||
"fix npt/sphere"_doc/fix_npt_sphere.html
|
"fix npt/sphere"_fix_npt_sphere.html
|
||||||
"fix npt/asphere"_doc/fix_npt_asphere.html
|
"fix npt/asphere"_fix_npt_asphere.html
|
||||||
"fix nph"_doc/fix_nph.html
|
"fix nph"_fix_nph.html
|
||||||
"fix press/berendsen"_doc/fix_press_berendsen.html :ul
|
"fix press/berendsen"_fix_press_berendsen.html :ul
|
||||||
|
|
||||||
|
The "fix npt"_fix_npt.html commands include a Nose-Hoover thermostat
|
||||||
|
and barostat. "Fix nph"_fix_nph.html is just a Nose/Hoover barostat;
|
||||||
|
it does no thermostatting. Both "fix nph"_fix_nph.html and "fix
|
||||||
|
press/bernendsen"_fix_press_berendsen.html can be used in conjunction
|
||||||
|
with any of the thermostatting fixes.
|
||||||
|
|
||||||
|
As with the thermostats, "fix npt"_fix_npt.html and "fix
|
||||||
|
nph"_fix_nph.html only use translational motion of the particles in
|
||||||
|
computing T and P and performing thermo/barostatting. "Fix
|
||||||
|
npt/sphere"_fix_npt_sphere.html and "fix
|
||||||
|
npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
|
||||||
|
translation velocities but also rotational velocities for spherical
|
||||||
|
and aspherical particles.
|
||||||
|
|
||||||
|
All of the barostatting fixes use the "compute
|
||||||
|
pressure"_compute_pressure.html compute to calculate a current
|
||||||
|
pressure. The barostatting fixes can also use temperature computes
|
||||||
|
that remove bias for the purpose of computing the current temperature
|
||||||
|
which contributes to the current pressure. See the doc pages for the
|
||||||
|
individual fixes and for the "fix_modify"_fix_modify.html command for
|
||||||
|
instructions on how to assign a temperature or pressure compute to a
|
||||||
|
barostatting fix.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix
|
||||||
|
npt"_fix_npt.html and "fix nph"_fix_nph.html) perform time
|
||||||
|
integration. "Fix press/berendsen"_fix_press_berendsen.html does NOT,
|
||||||
|
so it should be used with one of the constant NVE fixes or with one of
|
||||||
|
the NVT fixes.
|
||||||
|
|
||||||
|
Finally, thermodynamic output, which can be setup via the
|
||||||
|
"thermo_style"_thermo_style.html command, often includes temperature
|
||||||
|
and pressure values. As explained on the doc page for the
|
||||||
|
"thermo_style"_thermo_style.html command, the default T and P are
|
||||||
|
setup by the thermo command itself. They are NOT the ones associated
|
||||||
|
with any thermostatting or barostatting fix you have defined or with
|
||||||
|
any compute that calculates a temperature or pressure. Thus if you
|
||||||
|
want to view these values of T and P, you need to specify them
|
||||||
|
explicitly via a "thermo_style custom"_thermo_style.html command. Or
|
||||||
|
you can use the "thermo_modify"_thermo_modify.html command to
|
||||||
|
re-define what temperature or pressure compute is used for default
|
||||||
|
thermodynamic output.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
:line
|
:line
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue