forked from lijiext/lammps
118 lines
4.9 KiB
HTML
118 lines
4.9 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/cs command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<P>compute ID group-ID temp/cs group1 group2 pre
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</P>
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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/cs = style name of this compute command
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<LI>group1 = group-ID of either cores or shells
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<LI>group2 = group-ID of either shells or cores
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute oxygen_c-s all temp/cs O_core O_shell
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compute core_shells all temp/cs cores shells
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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 system based
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on the center-of-mass velocity of atom pairs that are bonded to each
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other. This compute is designed to be used with the adiabatic
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core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
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<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
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overview of the model as implemented in LAMMPS. Specifically, this
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compute enables correct temperature calculation and thermostatting of
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core/shell pairs where it is desirable for the internal degrees of
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freedom of the core/shell pairs to not be influenced by a thermostat.
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A compute of this style can be used by any command that computes a
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temperature via <A HREF = "fix_modify.html">fix_modify</A> e.g. <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>For this compute, core and shell particles are specified by two
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respective group IDs, which can be defined using the
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<A HREF = "group.html">group</A> command. The number of atoms in the two groups
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must be the same and there should be one bond defined between a pair
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of atoms in the two groups.
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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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the velocity of each core or shell atom used in the KE calculation is
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the velocity of the center-of-mass (COM) of the core/shell pair the
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atom is part of.
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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. Again, the velocity of each core or shell atom is its
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COM velocity.
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</P>
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<P>The change this fix makes to core/shell atom velocities 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. This "bias" is the velocity of the atom
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relative to the COM velocity of the core/shell pair. If this compute
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is used with a fix command that performs thermostatting then this bias
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will be subtracted from each atom, thermostatting of the remaining COM
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velocity will be performed, and the bias will be added back in. This
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means the thermostating will effectively be performed on the
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core/shell pairs, instead of on the individual core and shell atoms.
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Thermostatting fixes that work in this way include <A HREF = "fix_nh.html">fix
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nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
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temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
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langevin</A>.
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</P>
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<P>The internal energy of core/shell pairs can be calculated by the
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<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command, if chunks are
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defined as core/shell pairs. See <A HREF = "Section_howto.html#howto_25">Section_howto
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25</A> for more discussion on how to do this.
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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.
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</P>
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<P>The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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</P>
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<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
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vector values will be in energy <A HREF = "units.html">units</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The number of core/shell pairs contributing to the temperature is
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assumed to be constant for the duration of the run. No fixes should
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be used which generate new molecules or atoms during a simulation.
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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>, <A HREF = "compute_temp_chunk.html">compute
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temp/chunk</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "MitchellFinchham"></A>
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<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
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5, 1031-1038 (1993).
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</P>
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</HTML>
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