forked from lijiext/lammps
149 lines
4.9 KiB
Plaintext
149 lines
4.9 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute heat/flux command :h3
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[Syntax:]
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compute ID group-ID heat/flux pe-ID :pre
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ID, group-ID are documented in "compute"_compute.html command
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heat/flux = style name of this compute command
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pe-ID = ID of a compute that calculates per-atom potential energy :ul
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[Examples:]
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compute myFlux all heat/flux myPE :pre
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[Description:]
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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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See the "fix thermal/conductivity"_fix_thermal_conductivity.html
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command for details on how to compute thermal conductivity in an
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alternate way, via the Muller-Plathe method.
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The compute takes a {pe-ID} argument which is the ID of a "compute
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pe/atom"_compute_pe_atom.html that calculates per-atom potential
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energy. Normally, it should be defined for the same group used by
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compute heat/flux, though LAMMPS does not check for this.
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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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:c,image(Eqs/heat_flux_k.jpg)
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:c,image(Eqs/heat_flux_J.jpg)
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Ei is the per-atom energy (potential and kinetic). The potential
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portion is calculated by the compute {pe-ID} specified as an argument
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to the compute heat/flux command.
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IMPORTANT NOTE: The per-atom potential energy calculated by the
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{pe-ID} compute should only include pairwise energy, to be consistent
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with the second virial-like term in the formula for J. Thus if any
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bonds, angles, etc exist in the system, the compute should limit its
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calculation to only the pair contribution. E.g. it could be defined
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as follows. Note that if {pair} is not listed as the last argument,
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it will be included by default, but so will other contributions such
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as bond, angle, etc.
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compute myPE all pe/atom pair :pre
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The second term of the heat flux equation for J is calculated by
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compute heat/flux for pairwise interactions for any I,J pair where one
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of the 2 atoms in is the compute group. It can be output every so
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many timesteps (e.g. via the thermo_style custom command). Then as
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post-processing steps, an autocorrelation can be performed, its
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integral estimated, and the Green-Kubo formula evaluated.
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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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"correlate.py"_Scripts/correlate.py 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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correlate.py flux.log -c 3 -s 200 :pre
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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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"units"_units.html 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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[Output info:]
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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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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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[Restrictions:]
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Only pairwise interactions, as defined by the pair_style command, are
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included in this calculation.
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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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[Related commands:]
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"fix thermal/conductivity"_fix_thermal_conductivity.html
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[Default:] none
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:line
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Sample LAMMPS input script :h4
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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 :pre
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# ------------- Equilibration and thermalisation ---------------- :pre
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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 :pre
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# --------------- Equilibration in nve ----------------- :pre
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fix NVE all nve
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run 8000 :pre
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# -------------- Flux calculation in nve --------------- :pre
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reset_timestep 0
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compute myPE all pe/atom pair
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compute flux all heat/flux myPE
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log flux.log
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variable J equal c_flux\[1\]/vol
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thermo_style custom step temp v_J
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run 100000 :pre
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