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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2781 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-04-29 16:54:14 +00:00
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3
doc/Section_commands.html
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@ -345,7 +345,8 @@ description:
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -474,6 +474,7 @@ description:
"temp/com"_compute_temp_com.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html :tb(c=6,ea=c)

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doc/Section_howto.html
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@ -1178,6 +1178,7 @@ pressure</A> command calculates pressure.
<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_profile.html">compute temp/profile</A>
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
@ -1186,9 +1187,10 @@ 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.
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
@ -1203,7 +1205,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
</UL>
<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
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, 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
@ -1225,8 +1227,9 @@ the x and z components of velocity by using it in conjunction with
<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:
velocities; they do NOT perform time integration updates. 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>
@ -1258,12 +1261,15 @@ 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.
pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
pressure</A> command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet 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

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doc/Section_howto.txt
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@ -1169,6 +1169,7 @@ pressure"_compute_pressure.html command calculates pressure.
"compute temp/com"_compute_temp_com.html
"compute temp/deform"_compute_temp_deform.html
"compute temp/partial"_compute_temp_partial.html
"compute temp/profile"_compute_temp_profile.html
"compute temp/ramp"_compute_temp_ramp.html
"compute temp/region"_compute_temp_region.html :ul
@ -1177,9 +1178,10 @@ 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.
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
Thermostatting in LAMMPS is performed by "fixes"_fix.html. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
@ -1194,7 +1196,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
"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
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, 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
@ -1216,8 +1218,9 @@ the x and z components of velocity by using it in conjunction with
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:
velocities; they do NOT perform time integration updates. 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
@ -1249,12 +1252,15 @@ 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.
pressure. By default, this compute is created with a simple "compute
temp"_compute_temp.html (see the last argument of the "compute
pressure"_compute_pressure.html command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet 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

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doc/compute.html
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@ -130,6 +130,7 @@ available in LAMMPS:
<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles

1
doc/compute.txt
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@ -127,6 +127,7 @@ available in LAMMPS:
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles :ul

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doc/compute_temp_asphere.html
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@ -50,9 +50,11 @@ rotational motion to the extra degrees of freedom. E.g. the <A HREF = "pair_gay
pair potential</A> does not impart torque to spherical
particles, so they do not rotate.
</P>
<P>The rotational kinetic energy is computed as 1/2 I w^2, where I is the
inertia tensor for the aspherical particle and w is its angular
velocity, which is computed from its angular momentum.
<P>The translational kinetic energy is computed the same as is described
by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
for the aspherical particle and w is its angular velocity, which is
computed from its angular momentum.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be

8
doc/compute_temp_asphere.txt
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@ -47,9 +47,11 @@ rotational motion to the extra degrees of freedom. E.g. the "GayBerne
pair potential"_pair_gayberne.html does not impart torque to spherical
particles, so they do not rotate.
The rotational kinetic energy is computed as 1/2 I w^2, where I is the
inertia tensor for the aspherical particle and w is its angular
velocity, which is computed from its angular momentum.
The translational kinetic energy is computed the same as is described
by the "compute temp"_compute_temp.html command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
for the aspherical particle and w is its angular velocity, which is
computed from its angular momentum.
IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be

3
doc/compute_temp_com.html
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@ -33,7 +33,8 @@ command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
<P>After the center-of-mass velocity has been subtracted from each atom,
the temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.

3
doc/compute_temp_com.txt
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@ -30,7 +30,8 @@ command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
After the center-of-mass velocity has been subtracted from each atom,
the temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.

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doc/compute_temp_deform.html
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@ -36,10 +36,10 @@ that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</
<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The deformation fix changes the box size and/or shape over time, so
each point in the simulation box can be thought of as having a
each atom in the simulation box can be thought of as having a
"streaming" velocity. For example, if the box is being sheared in x,
relative to y, then points at the bottom of the box (low y) have a
small x velocity, while points at the top of the box (hi y) have a
relative to y, then atoms at the bottom of the box (low y) have a
small x velocity, while atoms at the top of the box (hi y) have a
large x velocity. This position-dependent streaming velocity is
subtracted from each atom's actual velocity to yield a thermal
velocity which is used to compute the temperature.
@ -56,11 +56,12 @@ not changed, and thus they do NOT have the streaming velocity assumed
by this compute. LAMMPS will warn you if fix deform is defined and
its remap setting is not consistent with this compute.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
v in the kinetic energy formula is the atom's thermal velocity.
<P>After the streaming velocity has been subtracted from each atom, the
temperature is calculated by the formula KE = dim/2 N k T, where KE =
total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
or 3 = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. Note that v in
the kinetic energy formula is the atom's thermal velocity.
</P>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
@ -104,8 +105,9 @@ the simulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform.html">fix
deform</A>, <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "compute_temp_profile.html">compute
temp/profile</A>, <A HREF = "fix_deform.html">fix deform</A>,
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_temp_deform.txt
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@ -33,10 +33,10 @@ that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The deformation fix changes the box size and/or shape over time, so
each point in the simulation box can be thought of as having a
each atom in the simulation box can be thought of as having a
"streaming" velocity. For example, if the box is being sheared in x,
relative to y, then points at the bottom of the box (low y) have a
small x velocity, while points at the top of the box (hi y) have a
relative to y, then atoms at the bottom of the box (low y) have a
small x velocity, while atoms at the top of the box (hi y) have a
large x velocity. This position-dependent streaming velocity is
subtracted from each atom's actual velocity to yield a thermal
velocity which is used to compute the temperature.
@ -53,11 +53,12 @@ not changed, and thus they do NOT have the streaming velocity assumed
by this compute. LAMMPS will warn you if fix deform is defined and
its remap setting is not consistent with this compute.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
v in the kinetic energy formula is the atom's thermal velocity.
After the streaming velocity has been subtracted from each atom, the
temperature is calculated by the formula KE = dim/2 N k T, where KE =
total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
or 3 = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. Note that v in
the kinetic energy formula is the atom's thermal velocity.
A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
@ -101,7 +102,8 @@ the simulation.
[Related commands:]
"compute temp/ramp"_compute_temp_ramp.html, "fix
deform"_fix_deform.html, "fix nvt/sllod"_fix_nvt_sllod.html
"compute temp/ramp"_compute_temp_ramp.html, "compute
temp/profile"_compute_temp_profile.html, "fix deform"_fix_deform.html,
"fix nvt/sllod"_fix_nvt_sllod.html
[Default:] none

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doc/compute_temp_ramp.html
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@ -28,20 +28,27 @@
</PRE>
<P><B>Examples:</B>
</P>
<PRE>temperature 2nd middle ramp vx 0 8 y 2 12 units lattice
<PRE>compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms, after subtracting out an imposed velocity on the system before
atoms, after subtracting out an ramped velocity profile before
computing the kinetic energy. A compute of this style can be used by
any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The meaning of the arguments for this command is the same as for the
<A HREF = "velocity.html">velocity ramp</A> command which was presumably used to
impose the velocity.
<P>The meaning of the arguments for this command which define the
velocity ramp are the same as for the <A HREF = "velocity.html">velocity ramp</A>
command which was presumably used to impose the velocity.
</P>
<P>After the ramp velocity has been subtracted from the specified
dimension for each atom, the temperature is calculated by the formula
KE = dim/2 N k T, where KE = total kinetic energy of the group of
atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
simulation, N = number of atoms in the group, k = Boltzmann constant,
and T = temperature.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for coordinates (c1,c2) and velocities (vlo,vhi). A <I>box</I> value
@ -93,8 +100,8 @@ the simulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_temp_deform.html">compute
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_profile.html">compute
temp/profie</A>, <A HREF = "compute_temp_deform.html">compute
temp/deform</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>

20
doc/compute_temp_ramp.txt
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@ -24,20 +24,27 @@ keyword = {units} :ul
[Examples:]
temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre
compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms, after subtracting out an imposed velocity on the system before
atoms, after subtracting out an ramped velocity profile before
computing the kinetic energy. A compute of this style can be used by
any command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The meaning of the arguments for this command is the same as for the
"velocity ramp"_velocity.html command which was presumably used to
impose the velocity.
The meaning of the arguments for this command which define the
velocity ramp are the same as for the "velocity ramp"_velocity.html
command which was presumably used to impose the velocity.
After the ramp velocity has been subtracted from the specified
dimension for each atom, the temperature is calculated by the formula
KE = dim/2 N k T, where KE = total kinetic energy of the group of
atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
simulation, N = number of atoms in the group, k = Boltzmann constant,
and T = temperature.
The {units} keyword determines the meaning of the distance units used
for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value
@ -90,11 +97,10 @@ the simulation.
[Related commands:]
"compute temp"_compute_temp.html, "compute
temp/region"_compute_temp_region.html, "compute
temp/profie"_compute_temp_profile.html, "compute
temp/deform"_compute_temp_deform.html, "compute
pressure"_compute_pressure.html
[Default:]
The option default is units = lattice.

7
doc/compute_temp_sphere.html
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@ -36,9 +36,10 @@ particles with only translational kinetic energy.
translational, 3 rotational). For 2d spherical particles, each has 3
degrees of freedom (2 translational, 1 rotational).
</P>
<P>The rotational kinetic energy is computed as 1/2 I w^2, where I is the
moment of inertia for a sphere and w is the particle's angular
velocity.
<P>The translational kinetic energy is computed the same as is described
by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the moment of
inertia for a sphere and w is the particle's angular velocity.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as spheres, not disks, meaning their moment of inertia will be the

7
doc/compute_temp_sphere.txt
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@ -33,9 +33,10 @@ For 3d spherical particles, each has 6 degrees of freedom (3
translational, 3 rotational). For 2d spherical particles, each has 3
degrees of freedom (2 translational, 1 rotational).
The rotational kinetic energy is computed as 1/2 I w^2, where I is the
moment of inertia for a sphere and w is the particle's angular
velocity.
The translational kinetic energy is computed the same as is described
by the "compute temp"_compute_temp.html command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the moment of
inertia for a sphere and w is the particle's angular velocity.
IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
as spheres, not disks, meaning their moment of inertia will be the

24
doc/fix_langevin.html
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@ -97,19 +97,17 @@ thermostatting.
run from <I>Tstart</I> to <I>Tstop</I>.
</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
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.
with <A HREF = "compute.html">compute commands</A> that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. 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: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
</P>
<P>The <I>damp</I> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0

24
doc/fix_langevin.txt
View File

@ -88,19 +88,17 @@ The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}.
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.
with "compute commands"_compute.html that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. 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: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
The {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0