forked from lijiext/lammps
128 lines
5.5 KiB
HTML
128 lines
5.5 KiB
HTML
<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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<H3>compute temp/asphere 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/asphere bias-ID
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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/asphere = style name of this compute command
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<LI>bias-ID = ID of a temperature compute that removes a velocity bias (optional)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all temp/asphere
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compute myTemp mobile temp/asphere tempCOM
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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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aspherical particles, including a contribution from both their
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translational and rotational kinetic energy. This differs from the
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usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
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particles with only translational kinetic energy.
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</P>
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<P>Only finite-size particles (aspherical or spherical) can be included
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in the group. For 3d finite-size particles, each has 6 degrees of
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freedom (3 translational, 3 rotational). For 2d finite-size
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particles, each has 3 degrees of freedom (2 translational, 1
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rotational).
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</P>
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<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
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all finite-size aspherical or spherical particles in your model will
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freely rotate, sampling all their rotational dof. It is possible to
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use a combination of interaction potentials and fixes that induce no
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torque or otherwise constrain some of all of your particles so that
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this is not the case. Then there are less dof and you should use the
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<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
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accordingly.
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</P>
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<P>For example, an aspherical particle with all three of its
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<A HREF = "shape.html">shape</A> parameters the same is a sphere. If it does not
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rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of
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3 in 2d). A uniaxial aspherical particle has two of its three shape
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parameters the same. If it does not rotate around the axis
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perpendicular to its circular cross section, then it should have 5 dof
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instead of 6 in 3d.
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</P>
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<P>The translational kinetic energy is computed the same as is described
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by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
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kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
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for the aspherical particle and w is its angular velocity, which is
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computed from its angular momentum.
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</P>
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<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
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as ellipsoids, not ellipses, meaning their moments of inertia will be
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the same as in 3d.
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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. The formula for the components of the
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tensor is the same as the above formula, except that v^2 and w^2 are
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replaced by vx*vy and wx*wy for the xy component, and the appropriate
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elements of the inertia tensor are used. The 6 components of the
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vector are ordered xx, yy, 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>If a <I>bias-ID</I> is specified it must be the ID of a temperature compute
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that removes a "bias" velocity from each atom. This allows compute
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temp/sphere to compute its thermal temperature after the translational
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kinetic energy components have been altered in a prescribed way,
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e.g. to remove a velocity profile. Thermostats that use this compute
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will work with this bias term. See the doc pages for individual
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computes that calculate a temperature and the doc pages for fixes that
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perform thermostatting for more details.
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</P>
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<P>This compute subtracts out translational degrees-of-freedom due to
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fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
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shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. This means the
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temperature of groups of atoms that include these constraints will be
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computed correctly. If needed, the subtracted degrees-of-freedom can
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be altered using the <I>extra</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
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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>
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</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.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The scalar value calculated by this compute is "intensive", meaning it
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is independent of the number of atoms in the simulation. The vector
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values are "extensive", meaning they scale with the number of atoms in
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the simulation.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This compute requires that particles be represented as extended
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ellipsoids and not point particles. This means they will have an
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angular momentum and a shape which is determined by the
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<A HREF = "shape.html">shape</A> command.
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</P>
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<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>
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</HTML>
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