mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6631 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
182a07a2a3
commit
a6aec34a91
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@ -362,9 +362,9 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
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package</A>.
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</P>
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||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD></TR>
|
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<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -389,7 +389,8 @@ each style or click on the style itself for a full description:
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<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
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</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
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</TD></TR></TABLE></DIV>
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<P>These are accelerated compute styles, which can be used if LAMMPS is
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|
|
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|||
|
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@ -500,6 +500,7 @@ package"_Section_accelerate.html.
|
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"freeze/cuda"_fix_freeze.html,
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"addforce/cuda"_fix_addforce.html,
|
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"addtorque"_fix_addtorque.html,
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"aveforce/cuda"_fix_aveforce.html,
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"enforce2d/cuda"_fix_enforce2d.html,
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"gravity/cuda"_fix_gravity.html,
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@ -576,7 +577,8 @@ These are compute styles contributed by users, which can be used if
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"ke/atom/eff"_compute_ke_atom_eff.html,
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"temp/eff"_compute_temp_eff.html,
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"temp/deform/eff"_compute_temp_deform_eff.html,
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"temp/region/eff"_compute_temp_region_eff.html :tb(c=6,ea=c)
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"temp/region/eff"_compute_temp_region_eff.html,
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"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
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These are accelerated compute styles, which can be used if LAMMPS is
|
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built with the "appropriate accelerated
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@ -818,5 +820,3 @@ package"_Section_accelerate.html.
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"pppm/cuda"_kspace_style.html,
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"pppm/gpu"_kspace_style.html :tb(c=4,ea=c)
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|
|
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|
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@ -0,0 +1,101 @@
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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>compute temp/rotate command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID temp/rotate
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>temp/rotate = style name of this compute command
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute Tbead bead temp/rotate
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the temperature of a group of
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atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
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This is useful if the group is expected to have a non-zero net
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velocity and/or global rotation motion for some reason. A compute of this style can be used by any
|
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command that computes a temperature,
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e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
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temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
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</P>
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<P>After the center-of-mass velocity and angular velocity has been subtracted from each atom,
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the temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in the group, k = Boltzmann constant, and T = temperature.
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</P>
|
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<P>A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
|
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.
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</P>
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<P>The number of atoms contributing to the temperature is assumed to be
|
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constant for the duration of the run; use the <I>dynamic</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
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</P>
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<P>The removal of the center-of-mass velocity and angular velocity by this fix is essentially
|
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computing the temperature after a "bias" has been removed from the
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velocity of the atoms. If this compute is used with a fix command
|
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that performs thermostatting then this bias will be subtracted from
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each atom, thermostatting of the remaining thermal velocity will be
|
||||
performed, and the bias will be added back in. Thermostatting fixes
|
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that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
|
||||
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
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langevin</A>.
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||||
</P>
|
||||
<P>This compute subtracts out degrees-of-freedom due to fixes that
|
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constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
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||||
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
|
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atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
|
||||
discussion of different ways to compute temperature and perform
|
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thermostatting.
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</P>
|
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<P><B>Output info:</B>
|
||||
</P>
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<P>This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
||||
section</A> for an overview of LAMMPS output
|
||||
options.
|
||||
</P>
|
||||
<P>The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
</P>
|
||||
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
|
||||
vector values will be in energy <A HREF = "units.html">units</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This compute is part of the "user-misc" package. It is only enabled
|
||||
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
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||||
</P>
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<P><A HREF = "compute_temp.html">compute temp</A>
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||||
</P>
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<P><B>Default:</B> none
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||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,96 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
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||||
:link(lc,Section_commands.html#comm)
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||||
|
||||
:line
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||||
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||||
compute temp/rotate command :h3
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||||
|
||||
[Syntax:]
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||||
|
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compute ID group-ID temp/rotate :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/rotate = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute Tbead bead temp/rotate :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the temperature of a group of
|
||||
atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
|
||||
This is useful if the group is expected to have a non-zero net
|
||||
velocity and/or global rotation motion for some reason. 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_nh.html, etc.
|
||||
|
||||
After the center-of-mass velocity and angular 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.
|
||||
|
||||
A kinetic energy tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute for use in the computation of a pressure
|
||||
tensor. The formula for the components of the tensor is the same as
|
||||
the above formula, except that v^2 is replaced by vx*vy for the xy
|
||||
component, etc. The 6 components of the vector are ordered xx, yy,
|
||||
zz, xy, xz, yz.
|
||||
|
||||
The number of atoms contributing to the temperature is assumed to be
|
||||
constant for the duration of the run; use the {dynamic} option of the
|
||||
"compute_modify"_compute_modify.html command if this is not the case.
|
||||
|
||||
The removal of the center-of-mass velocity and angular velocity by this fix is essentially
|
||||
computing the temperature after a "bias" has been removed from the
|
||||
velocity of the atoms. If this compute is used with a fix command
|
||||
that performs thermostatting then this bias will be subtracted from
|
||||
each atom, thermostatting of the remaining thermal velocity will be
|
||||
performed, and the bias will be added back in. Thermostatting fixes
|
||||
that work in this way include "fix nvt"_fix_nh.html, "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix
|
||||
temp/berendsen"_fix_temp_berendsen.html, and "fix
|
||||
langevin"_fix_langevin.html.
|
||||
|
||||
This compute subtracts out degrees-of-freedom due to fixes that
|
||||
constrain molecular motion, such as "fix shake"_fix_shake.html and
|
||||
"fix rigid"_fix_rigid.html. This means the temperature of groups of
|
||||
atoms that include these constraints will be computed correctly. If
|
||||
needed, the subtracted degrees-of-freedom can be altered using the
|
||||
{extra} option of the "compute_modify"_compute_modify.html command.
|
||||
|
||||
See "this howto section"_Section_howto.html#4_16 of the manual for a
|
||||
discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global scalar (the temperature) and a global
|
||||
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input. See "this
|
||||
section"_Section_howto.html#4_15 for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature "units"_units.html. The
|
||||
vector values will be in energy "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the "user-misc" package. It is only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html
|
||||
|
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[Default:] none
|
||||
|
|
@ -0,0 +1,101 @@
|
|||
<HTML>
|
||||
<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>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix addtorque command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID addtorque Tx Ty Tz
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>addtorque = style name of this fix command
|
||||
|
||||
<LI>Tx,Ty,Tz = torque component values (torque units)
|
||||
|
||||
<LI>any of Tx,Ty,Tz can be a variable (see below)
|
||||
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix kick bead addtorque 2.0 3.0 5.0
|
||||
fix kick bead addtorque 0.0 0.0 v_oscillate
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<UL><LI>Add a set of forces to each atom in
|
||||
the group such that:
|
||||
the components of the total torque applied on the group (around its center of mass) are Tx,Ty,Tz;
|
||||
|
||||
<LI>the group would move as a rigid body in the absence of other forces.
|
||||
|
||||
|
||||
</UL>
|
||||
<P>This command can be used to drive a group of atoms into rotation.
|
||||
</P>
|
||||
<P>Any of the 3 quantities defining the torque components can be specified
|
||||
as an equal-style <A HREF = "variable.html">variable</A>, namely <I>Tx</I>,
|
||||
<I>Ty</I>, <I>Tz</I>. 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
|
||||
torque component.
|
||||
</P>
|
||||
<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 torque.
|
||||
</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>energy</I> option is supported by this
|
||||
fix to add the potential "energy" inferred by the added forces to the
|
||||
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
|
||||
output</A>. This is a fictitious quantity but is
|
||||
needed so that the <A HREF = "minimize.html">minimize</A> command can include the
|
||||
forces added by this fix in a consistent manner. I.e. there is a
|
||||
decrease in potential energy when atoms move in the direction of the
|
||||
added forces.
|
||||
</P>
|
||||
<P>This fix computes a global scalar and a global 3-vector,
|
||||
which can be accessed by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. The scalar is the potential energy
|
||||
discussed above. The vector is the total torque on the group of atoms
|
||||
before the forces on individual atoms are changed by the fix. The
|
||||
scalar and vector values calculated by this fix are "extensive".
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command.
|
||||
</P>
|
||||
<P>The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This fix is part of the "user-misc" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_addforce.html">fix addforce</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
"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 addtorque command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID addtorque Tx Ty Tz :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
addtorque = style name of this fix command :l
|
||||
Tx,Ty,Tz = torque component values (torque units) :l
|
||||
any of Tx,Ty,Tz can be a variable (see below) :l
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix kick bead addtorque 2.0 3.0 5.0
|
||||
fix kick bead addtorque 0.0 0.0 v_oscillate :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Add a set of forces to each atom in
|
||||
the group such that:
|
||||
the components of the total torque applied on the group (around its center of mass) are Tx,Ty,Tz; :ulb,l
|
||||
the group would move as a rigid body in the absence of other forces. :l
|
||||
:ule
|
||||
This command can be used to drive a group of atoms into rotation.
|
||||
|
||||
Any of the 3 quantities defining the torque components can be specified
|
||||
as an equal-style "variable"_variable.html, namely {Tx},
|
||||
{Ty}, {Tz}. 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
|
||||
torque component.
|
||||
|
||||
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 torque.
|
||||
|
||||
: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 {energy} option is supported by this
|
||||
fix to add the potential "energy" inferred by the added forces to the
|
||||
system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html. This is a fictitious quantity but is
|
||||
needed so that the "minimize"_minimize.html command can include the
|
||||
forces added by this fix in a consistent manner. I.e. there is a
|
||||
decrease in potential energy when atoms move in the direction of the
|
||||
added forces.
|
||||
|
||||
This fix computes a global scalar and a global 3-vector,
|
||||
which can be accessed by various "output
|
||||
commands"_Section_howto.html#4_15. The scalar is the potential energy
|
||||
discussed above. The vector is the total torque on the group of atoms
|
||||
before the forces on individual atoms are changed by the fix. The
|
||||
scalar and vector values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the "minimize"_minimize.html command. You should not
|
||||
specify force components with a variable that has time-dependence for
|
||||
use with a minimizer, since the minimizer increments the timestep as
|
||||
the iteration count during the minimization.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the "user-misc" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix addforce"_fix_addforce.html
|
||||
|
||||
[Default:] none
|
||||
Loading…
Reference in New Issue