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lammps/examples/HEAT/in.lj_hex
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###############################################################################
#
#
# This input script is a modified version of the example script lj_hex.lmp
# which is part of the supplementary (open access) material of the paper
#
# P. Wirnsberger, D. Frenkel and C. Dellago,
# "An enhanced version of the heat exchange algorithm with excellent energy
# conservation properties", J. Chem. Phys. 143, 124104 (2015).
#
# The full article is available on arXiv: http://arxiv.org/pdf/1507.07081.
#
#
# Description:
# ------------
#
# This file is a LAMMPS input script for carrying out a NEMD simulation of
# Lennard-Jones using the HEX/a algorithm. The run produces two files:
# "out.Tlj_hex" contains the temperature profile and "out.Elj_hex" the time
# evolution of the total energy.
#
###############################################################################
log log.lj_hex
# heat flux
variable J equal 0.15
# timestep
variable dt equal 0.007
# cutoff radius for shifted LJ-potential
variable rc equal 3.0
# simulation time for the production run
variable tprod equal 5000
# total number of timesteps
variable Nprod equal floor(${tprod}/${dt})
# equilibrated steady state configuration
read_data "data.lj"
# use LJ shifted force pair style
pair_style lj/sf ${rc}
# with coefficients eps = 1, sigma = 1, and rc = 3.0
pair_coeff 1 1 1.0 1.0 ${rc}
# increase neigbor skin because of the large timestep
neighbor 0.8 bin
# options used for fix ave/time; sample the quantities every 10 steps
variable Nsamp equal 10
variable Nrepeat equal floor(${Nprod}/${Nsamp})
variable Nevery equal ${Nsamp}*${Nrepeat}
# box dimensions
variable Lz equal zhi-zlo
variable Lx equal xhi-xlo
variable Ly equal yhi-ylo
# reservoir width in z-direction
variable delta equal 2.
# specify z-extents of both reservoirs
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
variable zhi_Thi equal ${zlo_Thi}+${delta}
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
# resolution for fix ave/spatial
variable dz equal ${Lz}/60
# compute per-atom kinetic energy and temperature, respectively
# NOTE: In this example we ignored the centre of mass (com) velocities
# of the individual bins for simplicity. However, we took that
# into account for the publication.
compute ke all ke/atom
variable T atom c_ke/1.5
# specify the reservoirs
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
# compute the temperature of the individual region
compute cTlo all temp/region Tlo_region
compute cThi all temp/region Thi_region
# calculate the energy flux from the specified heat flux
variable F equal ${J}*${Lx}*${Ly}*2.
# use fix ehex to create the gradient
# hot reservoir
fix fHi all ehex 1 +${F} region Thi_region hex
# cold reservoir
fix fLo all ehex 1 -${F} region Tlo_region hex
# use velocity Verlet for integration
fix fNVEGrad all nve
# calculate the centre of mass velocity of the entire box (vcmx, vcmy, vcmz)
variable vcmx equal "vcm(all,x)"
variable vcmy equal "vcm(all,y)"
variable vcmz equal "vcm(all,z)"
variable vcm2 equal v_vcmx*v_vcmx+v_vcmy*v_vcmy+v_vcmz*v_vcmz
# specify the timestep
timestep ${dt}
# frequency for console output
thermo 10000
# print timestep, temperature, total energy and v_com^2 to console
thermo_style custom step temp etotal v_vcm2
# calculate spatial average of temperature
compute cchT all chunk/atom bin/1d z lower ${dz}
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
# compute the total energy
compute cKe all ke
compute cPe all pe
variable E equal c_cKe+c_cPe
# track the time evolution of the total energy
fix fE all ave/time ${Nsamp} 1000 10000 v_E file out.Elj_hex
# production run
run ${Nprod}
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