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