mirror of https://github.com/lammps/lammps.git
148 lines
5.0 KiB
HTML
148 lines
5.0 KiB
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 heat/flux 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 heat/flux pe-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>heat/flux = style name of this compute command
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<LI>pe-ID = ID of a compute that calculates per-atom potential energy
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute myFlux all heat/flux myPE
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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 heat flux vector based on
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interactions between atoms in the specified group. This can be used
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by itself to measure the heat flux between a hot and cold reservoir of
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particles or to calculate a thermal conductivity using the Green-Kubo
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formalism.
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</P>
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<P>The compute takes a <I>pe-ID</I> argument which is the ID of a <A HREF = "compute_pe_atom.html">compute
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pe/atom</A> that calculates per-atom potential
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energy. It should be defined for the same group used by compute
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heat/flux, though LAMMPS does not check for this.
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</P>
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<P>The Green-Kubo formulas relate the ensemble average of the
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auto-correlation of the heat flux J to the thermal conductivity kappa.
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</P>
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<CENTER><IMG SRC = "Eqs/heat_flux_k.jpg">
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</CENTER>
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<CENTER><IMG SRC = "Eqs/heat_flux_J.jpg">
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</CENTER>
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<P>Ei is the per-atom energy (potential and kinetic). The potential term
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is calculated by the compute <I>pe-ID</I> specified as an argument to
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the compute heat/flux command.
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</P>
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<P>IMPORTANT NOTE: The per-atom potential energy calculated by the
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<I>pe-ID</I> compute should only include pairwise energy, to be consistent
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with the full heat-flux calculation. Thus if any bonds, angles, etc
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exist in the system, the compute should limit its calculation to only
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the pair contribution. E.g. it could be defined as
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</P>
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<PRE>compute myPE all pe/atom pair
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</PRE>
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<P>Note that if <I>pair</I> is not listed as the last argument, it will be
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included by default, but so will other contributions such as bond,
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angle, etc.
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</P>
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<P>The heat flux J is calculated by this compute for pairwise
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interactions for any I,J pair where one of the 2 atoms in is the
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compute group. It can be output every so many timesteps (e.g. via the
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thermo_style custom command). Then as post-processing steps, an
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autocorrelation can be performed, its integral estimated, and the
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Green-Kubo formula evaluated.
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</P>
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<P>Here is an example of this procedure. First a LAMMPS input script for
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solid Ar is appended below. A Python script
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<A HREF = "Scripts/correlate.py">correlate.py</A> is also given, which calculates
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the autocorrelation of the flux output in the logfile flux.log,
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produced by the LAMMPS run. It is invoked as
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</P>
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<PRE>correlate.py flux.log -c 3 -s 200
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</PRE>
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<P>The resulting data lists the autocorrelation in column 1 and the
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integral of the autocorrelation in column 2. The integral of the
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correlation needs to be multiplied by V/(kB T^2) times the sample
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interval and the appropriate unit conversion factors. For real
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<A HREF = "units.html">units</A> in LAMMPS, this is 2917703220.0 in this case. The
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final thermal conductivity value obtained is 0.25 W/mK.
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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 vector of length 6. The 6 components are
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the x, y, z components of the full heat flux, followed by the x, y, z
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components of just the convective portion of the flux, which is the
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energy per atom times the velocity of the atom.
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</P>
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<P>The vector values calculated by this compute are "extensive", meaning
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they scale with the number of atoms in the simulation. They should be
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divided by the appropriate volume to get a flux.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>Only pairwise interactions, as defined by the pair_style command, are
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included in this calculation.
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</P>
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<P>To use this compute you must define an atom_style, such as dpd or
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granular, that communicates the velocites of ghost atoms.
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</P>
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<P><B>Related commands:</B> none
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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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<H4>Sample LAMMPS input script
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</H4>
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<PRE>atom_style dpd
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units real
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dimension 3
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boundary p p p
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lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 39.948
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pair_style lj/cut 13.0
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pair_coeff * * 0.2381 3.405
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group every region box
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velocity all create 70 102486 mom yes rot yes dist gaussian
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timestep 4.0
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thermo 10
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</PRE>
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<PRE># ------------- Equilibration and thermalisation ----------------
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</PRE>
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<PRE>fix NPT all npt 70 70 10 xyz 0.0 0.0 100.0 drag 0.2
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run 8000
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unfix NPT
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</PRE>
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<PRE># --------------- Equilibration in nve -----------------
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</PRE>
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<PRE>fix NVE all nve
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run 8000
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</PRE>
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<PRE># -------------- Flux calculation in nve ---------------
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</PRE>
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<PRE>reset_timestep 0
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compute flux all heat_flux
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log flux.log
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variable J equal c_flux<B>1</B>/vol
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thermo_style custom step temp v_J
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run 100000
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</PRE>
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</HTML>
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