2009-04-30 01:29:52 +08:00
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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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<HR>
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<H3>compute temp/profile 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/profile xflag yflag zflag binstyle args
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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/profile = style name of this compute command
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<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
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<LI>binstyle = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>xyz</I>
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<PRE> <I>x</I> arg = Nx
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<I>y</I> arg = Ny
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<I>z</I> arg = Nz
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<I>xy</I> args = Nx Ny
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<I>yz</I> args = Ny Nz
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<I>xz</I> args = Nx Nz
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<I>xyz</I> args = Nx Ny Nz
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Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
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</PRE>
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2012-11-27 02:29:40 +08:00
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>out</I>
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<PRE> <I>out</I> value = <I>tensor</I> or <I>bin</I>
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</PRE>
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2009-04-30 01:29:52 +08:00
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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 flow temp/profile 1 1 1 x 10
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2012-11-27 02:29:40 +08:00
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compute myTemp flow temp/profile 1 1 1 x 10 out bin
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2009-04-30 01:29:52 +08:00
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compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
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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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2013-07-24 22:24:17 +08:00
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atoms, after subtracting out a spatially-averaged center-of-mass
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velocity field, before computing the kinetic energy. This can be
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useful for thermostatting a collection of atoms undergoing a complex
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flow, e.g. via a profile-unbiased thermostat (PUT) as described in
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2009-04-30 01:29:52 +08:00
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<A HREF = "#Evans">(Evans)</A>. A compute of this style can 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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2010-04-03 00:51:06 +08:00
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<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
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2009-04-30 01:29:52 +08:00
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</P>
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<P>The <I>xflag</I>, <I>yflag</I>, <I>zflag</I> settings determine which components of
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2009-04-30 01:41:26 +08:00
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average velocity are subtracted out.
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2009-04-30 01:29:52 +08:00
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</P>
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<P>The <I>binstyle</I> setting and its <I>Nx</I>, <I>Ny</I>, <I>Nz</I> arguments determine
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how bins are setup to perform spatial averaging. "Bins" can be 1d
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slabs, 2d pencils, or 3d bricks depending on which <I>binstyle</I> is used.
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The simulation box is partitioned conceptually into <I>Nx</I> by <I>Ny</I> by
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<I>Nz</I> bins. Depending on the <I>binstyle</I>, you may only specify one or
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two of these values; the others are effectively set to 1 (no binning
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in that dimension). For non-orthogonal (triclinic) simulation boxes,
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the bins are "tilted" slabs or pencils or bricks that are parallel to
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the tilted faces of the box. See the <A HREF = "region.html">region prism</A>
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command for a discussion of the geometry of tilted boxes in LAMMPS.
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</P>
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2013-07-24 22:24:17 +08:00
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<P>When a temperature is computed, the center-of-mass velocity for the
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set of atoms that are both in the compute group and in the same
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spatial bin is calculated. This bias velocity is then subtracted from
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the velocities of individual atoms in the bin to yield a thermal
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velocity for each atom. Note that if there is only one atom in the
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bin, its thermal velocity will thus be 0.0.
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2009-04-30 01:29:52 +08:00
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</P>
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<P>After the spatially-averaged velocity field has been subtracted from
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2015-04-12 07:25:39 +08:00
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each atom, the temperature is calculated by the formula KE = (dim/2 N
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- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
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atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
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simulation, N = number of atoms in the group, k = Boltzmann constant,
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and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom
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subtracted to adjust for the removal of the center-of-mass velocity in
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each of Nx*Ny*Nz bins, as discussed in the <A HREF = "#Evans">(Evans)</A> paper.
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2009-04-30 01:29:52 +08:00
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</P>
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2012-11-27 02:29:40 +08:00
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<P>If the <I>out</I> keyword is used with a <I>tensor</I> value, which is the
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default, a kinetic energy tensor, stored as a 6-element vector, is
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also calculated by this compute for use in the computation of a
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pressure tensor. The formula for the components of the tensor is the
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same as the above formula, except that v^2 is replaced by vx*vy for
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the xy component, etc. The 6 components of the vector are ordered xx,
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yy, zz, xy, xz, yz.
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</P>
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<P>If the <I>out</I> keyword is used with a <I>bin</I> value, the count of atoms
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and computed temperature for each bin are stored for output, as an
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2012-11-27 02:34:06 +08:00
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array of values, as described below. The temperature of each bin is
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calculated as described above, where the bias velocity is subtracted
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and only the remaining thermal velocity of atoms in the bin
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contributes to the temperature. See the note below for how the
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temperature is normalized by the degrees-of-freedom of atoms in the
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bin.
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2009-04-30 01:29:52 +08:00
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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 spatially-averaged velocity field by this fix is
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essentially computing the temperature after a "bias" has been removed
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from the velocity of the atoms. If this compute is used with a fix
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command that performs thermostatting then this bias will be subtracted
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from each atom, thermostatting of the remaining thermal velocity will
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be performed, and the bias will be added back in. Thermostatting
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2010-04-03 00:51:06 +08:00
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fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
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2010-05-07 23:11:21 +08:00
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temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
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2009-04-30 01:29:52 +08:00
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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>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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2012-11-27 02:29:40 +08:00
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<P>IMPORTANT NOTE: When using the <I>out</I> keyword with a value of <I>bin</I>,
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the calculated temperature for each bin does not include the
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degrees-of-freedom adjustment described in the preceeding paragraph,
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for fixes that constrain molecular motion. It does include the
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adjustment due to the <I>extra</I> option, which is applied to each bin.
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</P>
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2011-08-26 01:01:01 +08:00
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<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
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a discussion of different ways to compute temperature and perform
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2009-04-30 01:29:52 +08:00
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thermostatting. Using this compute in conjunction with a
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2009-05-01 00:53:04 +08:00
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thermostatting fix, as explained there, will effectively implement a
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profile-unbiased thermostat (PUT), as described in <A HREF = "#Evans">(Evans)</A>.
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2009-04-30 01:29:52 +08:00
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</P>
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<P><B>Output info:</B>
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</P>
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2012-11-27 02:29:40 +08:00
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<P>This compute calculates a global scalar (the temperature). Depending
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on the setting of the <I>out</I> keyword, it also calculates a global
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vector or array. For <I>out</I> = <I>tensor</I>, it calculates a vector of
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length 6 (KE tensor), which can be accessed by indices 1-6. For <I>out</I>
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= <I>bin</I> it calculates a global array which has 2 columns and N rows,
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where N is the number of bins. The first column contains the number
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of atoms in that bin. The second contains the temperature of that
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bin, calculated as described above. The ordering of rows in the array
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is as follows. Bins in x vary fastest, then y, then z. Thus for a
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10x10x10 3d array of bins, there will be 1000 rows. The bin with
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indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
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+ ix = 322, where the rows are numbered from 1 to 1000 and the bin
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indices are numbered from 1 to 10 in each dimension.
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</P>
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<P>These values can be used by any command that uses global scalar or
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vector or array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
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2009-12-04 07:58:11 +08:00
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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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2010-03-03 05:51:16 +08:00
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<P>The scalar value calculated by this compute is "intensive". The
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2012-11-27 02:29:40 +08:00
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vector values are "extensive". The array values are "intensive".
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2009-04-30 01:29:52 +08:00
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</P>
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2010-01-24 07:20:05 +08:00
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<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
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2012-11-27 02:29:40 +08:00
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vector values will be in energy <A HREF = "units.html">units</A>. The first column
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of array values are counts; the values in the second column will be in
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temperature <A HREF = "units.html">units</A>.
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2010-01-24 07:20:05 +08:00
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</P>
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2009-04-30 01:29:52 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>You should not use too large a velocity-binning grid, especially in
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3d. In the current implementation, the binned velocity averages are
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summed across all processors, so this will be inefficient if the grid
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is too large, and the operation is performed every timestep, as it
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will be for most thermostats.
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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_ramp.html">compute
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temp/ramp</A>, <A HREF = "compute_temp_deform.html">compute
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temp/deform</A>, <A HREF = "compute_pressure.html">compute
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pressure</A>
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</P>
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<P><B>Default:</B>
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</P>
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2012-11-27 02:29:40 +08:00
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<P>The option default is out = tensor.
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2009-04-30 01:29:52 +08:00
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</P>
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<HR>
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<A NAME = "Evans"></A>
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<P><B>(Evans)</B> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
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</P>
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</HTML>
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