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@ -1019,78 +1019,137 @@ frequencies and global vs per-atom attributes are the same.
<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
</H4>
<P> add a HowTo on time integration options and/or thermostat/temperature options
4 thermostats
which do integration, which need fix nve or fix nph
all can be used with press/berendsen
only NVT thermostats rotational degrees of freedom directly
what bias is, how to remove it
howto remove bias for temp/sphere and temp/asphere
which biases can be doubled up via compute_modify bias command
<P>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.
</P>
<P>Enhanced the computes that calculate temperature, thermostatting
fixes, and time integrators that use temperature control to be more
flexible and consistent. This is for point particles, extended
spherical particles, and <A HREF = "doc/Section_howto.html#4_14">aspherical
particles</A>. Also Added new <A HREF = "doc/compute_ke.html">compute
ke</A> and <A HREF = "doc/compute_erotate_asphere.html">compute
erotate/asphere</A> commands.
<P>Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
</P>
<P>These <A HREF = "doc/compute.html">compute commands</A> calculate temperature. All
but the first 3 calculate velocity biases that are removed when
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.
<P>LAMMPS has several options for computing temperatures and for using
them in thermostatting and barostatting.
</P>
<UL><LI><A HREF = "doc/compute_temp.html">compute temp</A>
<LI><A HREF = "doc/compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "doc/compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "doc/compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "doc/compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "doc/compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "doc/compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "doc/compute_temp_region.html">compute temp/region</A>
<P>These <A HREF = "compute.html">compute commands</A> calculate temperature.
</P>
<UL><LI><A HREF = "compute_temp.html">compute temp</A>
<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
<P>Four thermostatting methods are available: Nose-Hoover, Berendsen,
Langevin, and direct rescaling. Nose/Hoover works on rotational
degrees-of-freedom for spherical and aspherical particles; the others
only work on translational degrees of freedom. Any of these methods
can use temperature computes that remove bias for the purpose of
computing the current temperature and performing thermostatting only
on the remaining thermal velocity. For <A HREF = "doc/Section_howto.html#4_13">non-equilibrium MD
simulations</A>., there is also a SLLOD fix
which does NVT thermostatting in conjunction with the SLLOD equations
of motion. These are the relevant <A HREF = "doc/fix.html">fix commands</A>:
<P>All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
temp/asphere</A> compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, another temperature compute that
subtracts a velocity bias, so the translational velocity of extended
spherical or aspherical particles can be adjusted in prescribed ways.
</P>
<UL><LI><A HREF = "doc/fix_nvt.html">fix nvt</A>
<LI><A HREF = "doc/fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "doc/fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "doc/fix_nvt_sllod.html">fix nvt/sllod</A>
<LI><A HREF = "doc/fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "doc/fix_langevin.html">fix langevin</A>
<LI><A HREF = "doc/fix_temp_rescale.html">fix temp/rescale</A>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
Berendsen, Langevin, and direct rescaling (temp/rescale):
</P>
<UL><LI><A HREF = "fix_nvt.html">fix nvt</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "fix_langevin.html">fix langevin</A>
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
</UL>
<P>Note that only the nvt fixes perform time integration. The others
should be used with an NVE integration fix such as these:
<P><A HREF = "fix_nvt.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> 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 <A HREF = "#4_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
nvt/asphere</A> thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
</P>
<UL><LI><A HREF = "doc/fix_nve.html">fix nve</A>
<LI><A HREF = "doc/fix_nve_sphere.html">fix nve/sphere</A>
<P>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 <A HREF = "fix_modify.html">fix_modify</A>
command for instructions on how to assign a temperature compute to a
thermostatting fix.
</P>
<P>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:
</P>
<UL><LI><A HREF = "fix_nve.html">fix nve</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "doc_fix_nve_asphere.html">fix nve/asphere</A>
</UL>
<P>Two barosttating methods are available: Nose-Hoover and Berendsen.
The fix npt commands include Nose-Hoover thermostatting. Fix nph and
fix press/bernendsen can be used in conjunction with any of the 4
thermostatting methods. These are the relevant <A HREF = "doc/fix.html">fix
commands</A>:
<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
</P>
<UL><LI><A HREF = "doc/fix_npt.html">fix npt</A>
<LI><A HREF = "doc/fix_npt_sphere.html">fix npt/sphere</A>
<LI><A HREF = "doc/fix_npt_asphere.html">fix npt/asphere</A>
<LI><A HREF = "doc/fix_nph.html">fix nph</A>
<LI><A HREF = "doc/fix_press_berendsen.html">fix press/berendsen</A>
<UL><LI><A HREF = "fix_npt.html">fix npt</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
<LI><A HREF = "fix_nph.html">fix nph</A>
<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
</UL>
<P>The <A HREF = "fix_npt.html">fix npt</A> commands include a Nose-Hoover thermostat
and barostat. <A HREF = "fix_nph.html">Fix nph</A> is just a Nose/Hoover barostat;
it does no thermostatting. Both <A HREF = "fix_nph.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
press/bernendsen</A> can be used in conjunction
with any of the thermostatting fixes.
</P>
<P>As with the thermostats, <A HREF = "fix_npt.html">fix npt</A> and <A HREF = "fix_nph.html">fix
nph</A> only use translational motion of the particles in
computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
npt/asphere</A> thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.
</P>
<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
pressure</A> 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 <A HREF = "fix_modify.html">fix_modify</A> command for
instructions on how to assign a temperature or pressure compute to a
barostatting fix.
</P>
<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_npt.html">fix
npt</A> and <A HREF = "fix_nph.html">fix nph</A>) perform time
integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.
</P>
<P>Finally, thermodynamic output, which can be setup via the
<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
and pressure values. As explained on the doc page for the
<A HREF = "thermo_style.html">thermo_style</A> 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 <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
re-define what temperature or pressure compute is used for default
thermodynamic output.
</P>
<HR>
<HR>

179
doc/Section_howto.txt
View File

@ -1010,79 +1010,136 @@ run every: any variable: nevery: screen, log: nevery :tb(s=:)
4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
add a HowTo on time integration options and/or thermostat/temperature options
4 thermostats
which do integration, which need fix nve or fix nph
all can be used with press/berendsen
only NVT thermostats rotational degrees of freedom directly
what bias is, how to remove it
howto remove bias for temp/sphere and temp/asphere
which biases can be doubled up via compute_modify bias command
Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.
Enhanced the computes that calculate temperature, thermostatting
fixes, and time integrators that use temperature control to be more
flexible and consistent. This is for point particles, extended
spherical particles, and "aspherical
particles"_doc/Section_howto.html#4_14. Also Added new "compute
ke"_doc/compute_ke.html and "compute
erotate/asphere"_doc/compute_erotate_asphere.html commands.
Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
These "compute commands"_doc/compute.html calculate temperature. All
but the first 3 calculate velocity biases that are removed when
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.
LAMMPS has several options for computing temperatures and for using
them in thermostatting and barostatting.
"compute temp"_doc/compute_temp.html
"compute temp/sphere"_doc/compute_temp_sphere.html
"compute temp/asphere"_doc/compute_temp_asphere.html
"compute temp/com"_doc/compute_temp_com.html
"compute temp/deform"_doc/compute_temp_deform.html
"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
These "compute commands"_compute.html calculate temperature.
Four thermostatting methods are available: Nose-Hoover, Berendsen,
Langevin, and direct rescaling. Nose/Hoover works on rotational
degrees-of-freedom for spherical and aspherical particles; the others
only work on translational degrees of freedom. Any of these methods
can use temperature computes that remove bias for the purpose of
computing the current temperature and performing thermostatting only
on the remaining thermal velocity. For "non-equilibrium MD
simulations"_doc/Section_howto.html#4_13., there is also a SLLOD fix
which does NVT thermostatting in conjunction with the SLLOD equations
of motion. These are the relevant "fix commands"_doc/fix.html:
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
"compute temp/com"_compute_temp_com.html
"compute temp/deform"_compute_temp_deform.html
"compute temp/partial"_compute_temp_partial.html
"compute temp/ramp"_compute_temp_ramp.html
"compute temp/region"_compute_temp_region.html :ul
"fix nvt"_doc/fix_nvt.html
"fix nvt/sphere"_doc/fix_nvt_sphere.html
"fix nvt/asphere"_doc/fix_nvt_asphere.html
"fix nvt/sllod"_doc/fix_nvt_sllod.html
"fix temp/berendsen"_doc/fix_temp_berendsen.html
"fix langevin"_doc/fix_langevin.html
"fix temp/rescale"_doc/fix_temp_rescale.html :ul
All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
"Fix temp/sphere"_fix_temp_sphere.html and "fix
temp/asphere"_fix_temp_asphere.html compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, another temperature compute that
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
should be used with an NVE integration fix such as these:
Thermostatting in LAMMPS is performed by "fixes"_fix.html. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
Berendsen, Langevin, and direct rescaling (temp/rescale):
"fix nve"_doc/fix_nve.html
"fix nve/sphere"_doc/fix_nve_sphere.html
"fix nvt"_fix_nvt.html
"fix nvt/sphere"_fix_nvt_sphere.html
"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
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
Two barosttating methods are available: Nose-Hoover and Berendsen.
The fix npt commands include Nose-Hoover thermostatting. Fix nph and
fix press/bernendsen can be used in conjunction with any of the 4
thermostatting methods. These are the relevant "fix
commands"_doc/fix.html:
Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
"fix npt"_doc/fix_npt.html
"fix npt/sphere"_doc/fix_npt_sphere.html
"fix npt/asphere"_doc/fix_npt_asphere.html
"fix nph"_doc/fix_nph.html
"fix press/berendsen"_doc/fix_press_berendsen.html :ul
"fix npt"_fix_npt.html
"fix npt/sphere"_fix_npt_sphere.html
"fix npt/asphere"_fix_npt_asphere.html
"fix nph"_fix_nph.html
"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.
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