forked from lijiext/lammps
89 lines
3.9 KiB
HTML
89 lines
3.9 KiB
HTML
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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/deform 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/deform
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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/deform = 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 myTemp all temp/deform myDeform
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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 a streaming velocity induced by the
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simulation box changing size and/or shape, for example in a
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non-equilibrium MD (NEMD) simulation. The size/shape change is
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induced by use of the <A HREF = "fix_deform.html">fix deform</A> command. A compute
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of this style is created by the <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
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command to compute the thermal temperature of atoms for thermostatting
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purposes. A compute of this style can also be used by any command
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that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>,
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<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
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</P>
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<P>The deformation fix changes the box size and/or shape over time, so
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each point in the simulation box can be thought of as having a
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"streaming" velocity. For example, if the box is being sheared in x,
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relative to y, then points at the bottom of the box (low y) have a
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small x velocity, while points at the top of the box (hi y) have a
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large x velocity. This position-dependent streaming velocity is
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subtracted from each atom's actual velocity to yield a thermal
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velocity which is used to compute the temperature.
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</P>
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<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
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remapping either atom coordinates or velocities to the changing
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simulation box. To use this compute, the fix should NOT remap atom
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positions, but rather should let atoms respond to the changing box by
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adjusting their own velocities (or let fix deform remap the atom
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velocities). If the fix does remap atom positions, their velocity is
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not changed, and thus they do not have the streaming velocity assumed
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by this compute. LAMMPS will warn you if this setting is not
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consistent.
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</P>
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<P>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. Note that
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v in the kinetic energy formula is the atom's thermal velocity.
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</P>
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<P>A 6-component kinetic energy tensor is also calculated by this compute
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for use in the computation of a pressure tensor. The formula for the
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components of the tensor is the same as the above formula, except that
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v^2 is replaced by vx * vy for the xy component, etc.
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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>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
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needed, the subtracted degrees-of-freedom can be altered using the
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<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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<P><B>Restrictions:</B> none
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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_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform.html">fix
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deform</A>, <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</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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