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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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2015-07-30 22:38:28 +08:00
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<HR>
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<H3>compute temp/chunk 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/chunk chunkID value1 value2 ... keyword value ...
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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/chunk = style name of this compute command
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<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
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<LI>zero or more values can be listed as value1,value2,etc
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<LI>value = <I>temp</I> or <I>kecom</I> or <I>internal</I>
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<PRE> temp = temperature of each chunk
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kecom = kinetic energy of each chunk based on velocity of center of mass
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internal = internal kinetic energy of each chunk
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>com</I> or <I>bias</I> or <I>adof</I> or <I>cdof</I>
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<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
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yes = subtract center-of-mass velocity from each chunk before calculating temperature
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no = do not subtract center-of-mass velocity
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<I>bias</I> value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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<I>adof</I> value = dof_per_atom
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dof_per_atom = define this many degrees-of-freedom per atom
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<I>cdof</I> value = dof_per_chunk
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dof_per_chunk = define this many degrees-of-freedom per chunk
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</PRE>
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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 fluid temp/chunk molchunk
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compute 1 fluid temp/chunk molchunk temp internal
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compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0
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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 that are also in chunks, after optionally subtracting out the
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center-of-mass velocity of each chunk. By specifying optional values,
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it can also calulate the per-chunk temperature or energies of the
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multiple chunks of atoms.
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</P>
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<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
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23</A> for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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</P>
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<P>The temperature is calculated by the formula KE = DOF/2 k T, where KE =
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total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
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v^2), DOF = the total number of degrees of freedom for those atoms, k
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= Boltzmann constant, and T = temperature.
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</P>
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<P>The DOF is calculated as N*adof + Nchunk*cdof, where N = number of
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atoms contributing to the KE, adof = degrees of freedom per atom, and
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cdof = degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the <A HREF = "dimension.html">dimension</A>
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command, and cdof = 0.0. This gives the usual formula for
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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>Note that the number of atoms contributing to the temperature is
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calculated each time the temperature is evaluated since it is assumed
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the atoms may be dynamically assigned to chunks. Thus there is no
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need to use the <I>dynamic</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command for this compute style.
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</P>
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<P>If any optional values are specified, then per-chunk quantities are
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also calculated and stored in a global array, as described below.
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</P>
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<P>The <I>temp</I> value calculates the temperature for each chunk by the
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formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk
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of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of
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freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.
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</P>
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<P>The DOF in this case is calculated as N*adof + cdof, where N = number
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of atoms in the chunk, adof = degrees of freedom per atom, and cdof =
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degrees of freedom per chunk. By default adof = 2 or 3 =
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dimensionality of system, as set via the <A HREF = "dimension.html">dimension</A>
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command, and cdof = 0.0. This gives the usual formula for
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temperature.
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</P>
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<P>The <I>kecom</I> value calculates the kinetic energy of each chunk as if
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all its atoms were moving with the velocity of the center-of-mass of
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the chunk.
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</P>
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<P>The <I>internal</I> value calculates the internal kinetic energy of each
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chunk. The interal KE is summed over the atoms in the chunk using an
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internal "thermal" velocity for each atom, which is its velocity minus
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the center-of-mass velocity of the chunk.
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</P>
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<HR>
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<P>Note that currently the global and per-chunk temperatures calculated
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by this compute only include translational degrees of freedom for each
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atom. No rotational degrees of freedom are included for finite-size
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particles. Also no degrees of freedom are subtracted for any velocity
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bias or constraints that are applied, such as <A HREF = "compute_temp_partial.html">compute
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temp/partial</A>, or <A HREF = "fix_shake.html">fix shake</A>
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or <A HREF = "fix_rigid.html">fix rigid</A>. This is because those degrees of
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freedom (e.g. a constrained bond) could apply to sets of atoms that
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are both included and excluded from a specific chunk, and hence the
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concept is somewhat ill-defined. In some cases, you can use the
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<I>adof</I> and <I>cdof</I> keywords to adjust the calculated degress of freedom
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appropriately, as explained below.
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</P>
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<P>Note that the per-chunk temperature calulated by this compute and the
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<A HREF = "fix_ave_chunk.html">fix ave/chunk temp</A> command can be different.
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This compute calculates the temperature for each chunk for a single
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snapshot. Fix ave/chunk can do that but can also time average those
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values over many snapshots, or it can compute a temperature as if the
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atoms in the chunk on different timesteps were collected together as
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one set of atoms to calculate their temperature. This compute allows
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the center-of-mass velocity of each chunk to be subtracted before
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calculating the temperature; fix ave/chunk does not.
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</P>
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<P>IMPORTANT NOTE: Only atoms in the specified group contribute to the
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calculations performed by this compute. The <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command defines its own group;
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atoms will have a chunk ID = 0 if they are not in that group,
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signifying they are not assigned to a chunk, and will thus also not
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contribute to this calculation. You can specify the "all" group for
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this command if you simply want to include atoms with non-zero chunk
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IDs.
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</P>
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<P>The simplest way to output the per-chunk results of the compute
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temp/chunk calculation to a file is to use the <A HREF = "fix_ave_time.html">fix
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ave/time</A> command, for example:
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</P>
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<PRE>compute cc1 all chunk/atom molecule
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compute myChunk all temp/chunk cc1 temp
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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</PRE>
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<HR>
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<P>The keyword/value option pairs are used in the following ways.
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</P>
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<P>The <I>com</I> keyword can be used with a value of <I>yes</I> to subtract the
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velocity of the center-of-mass for each chunk from the velocity of the
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atoms in that chunk, before calculating either the global or per-chunk
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temperature. This can be useful if the atoms are streaming or
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otherwise moving collectively, and you wish to calculate only the
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thermal temperature.
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</P>
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<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
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compute that removes a "bias" velocity from each atom. This also
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allows calculation of the global or per-chunk temperature using only
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the thermal temperature of atoms in each chunk 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. It also applies to the calculation
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of the other per-chunk values, such as <I>kecom</I> or <I>internal</I>, which
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involve the center-of-mass velocity of each chunk, which is calculated
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after the velocity bias is removed from each atom. Note that the
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temperature compute will apply its bias globally to the entire system,
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not on a per-chunk basis.
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</P>
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<P>The <I>adof</I> and <I>cdof</I> keywords define the values used in the degree of
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freedom (DOF) formulas used for the global or per-chunk temperature,
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as described above. They can be used to calculate a more appropriate
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temperature for some kinds of chunks. Here are 3 examples:
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</P>
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<P>If spatially binned chunks contain some number of water molecules and
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<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
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you could calculate a temperature with 6 degrees of freedom (DOF) (3
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translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
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</P>
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<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
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<I>bias</I> keyword to only allow the x component of velocity to contribute
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to the temperature, then <I>adof</I> = 1.0 would be appropriate.
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</P>
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<P>If each chunk consists of a large molecule, with some number of its
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bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
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by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
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set to the remaining degrees of freedom for the entire molecule
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(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
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molecule.
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</P>
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<HR>
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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#howto_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>This compute also optionally calculates a global array, if one or more
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of the optional values are specified. The number of rows in the array
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= the number of chunks <I>Nchunk</I> as calculated by the specified
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<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. The number of
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columns is the number of specifed values (1 or more). These values
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can be accessed by any command that uses global array values from a
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compute as input. Again, see <A HREF = "Section_howto.html#howto_15">Section_howto
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15</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". The
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vector values are "extensive". The array values are "intensive".
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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>. The array values
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will be in temperature <A HREF = "units.html">units</A> for the <I>temp</I> value, and in
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energy <A HREF = "units.html">units</A> for the <I>kecom</I> and <I>internal</I> values.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>com</I> and <I>bias</I> keywords cannot be used together.
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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 = "fix_ave_chunk.html">fix ave/chunk
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temp</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are com no, no bias, adof = dimensionality of the
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system (2 or 3), and cdof = 0.0.
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</P>
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</HTML>
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