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###############################################################################
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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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###############################################################################
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#
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#
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# This input script is a modified version of the example script lj_hex.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 HEX/a algorithm. The run produces two files:
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# "out.Tlj_hex" contains the temperature profile and "out.Elj_hex" 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_hex
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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 hex
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# cold reservoir
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fix fLo all ehex 1 -${F} region Tlo_region hex
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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_hex
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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_hex
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# production run
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run ${Nprod}
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###############################################################################
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#
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#
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# This input script is a modified version of the example script spce_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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# SPC/E water using the eHEX/a algorithm. The run produces two files:
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# "out.Tspce_ehex" contains the temperature profile and "out.Espce_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.spce_ehex
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# energy flux into the reservoir
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variable F equal 0.075
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# timestep
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variable dt equal 3.0
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# simulation time for the production run (1 ns)
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variable tprod equal 1000000
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# total number of timesteps
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variable Nprod equal floor(${tprod}/${dt})
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# parameters for the SPC/E model
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variable epsOO equal 0.15535
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variable sigOO equal 3.166
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variable theta equal 109.47
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# long-range and short-range cutoffs, respectively
|
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variable cutC equal (xhi-xlo)/2.
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variable cutLJ equal 11
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|
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# specification of units, spatial dimensions, boundary conditions and atom-style
|
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units real
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dimension 3
|
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boundary p p p
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atom_style full
|
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read_data "data.spce"
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# group atoms to molecules
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group O type 2
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group H type 1
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group water type 1 2
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# define the pair style with long-range Coulomb interaction
|
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# and short-range LJ interaction
|
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pair_style lj/cut/coul/long ${cutLJ} ${cutC}
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pair_coeff 2 2 ${epsOO} ${sigOO}
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pair_coeff 1 2 0 0
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pair_coeff 1 1 0 0
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|
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# use Ewald summation with a precision of 1.e-5
|
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kspace_style ewald 1.e-5
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# use harmonic bonds between sites of a molecules
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# NOTE: this will not have any effects as we use RATTLE to keep the bonds fixed,
|
||||
# but it is recommended.
|
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bond_style harmonic
|
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angle_style harmonic
|
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 ${theta}
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|
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# increase neigbor skin because of the large timestep
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neighbor 4.5 bin
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|
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# use standard correction terms for the truncated tail of the LJ potential
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pair_modify tail yes
|
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|
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variable Nsamp equal 10
|
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variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
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variable Nevery equal ${Nsamp}*${Nrepeat}
|
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|
||||
# compute the centre of mass velocity of the box (vcmx, vcmy, vcmz)
|
||||
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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|
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# compute temperature, pressure, potential energy, kinetic energy and total energy
|
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compute cT all temp
|
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compute cP all pressure thermo_temp
|
||||
compute cPe all pe
|
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compute cKe all ke
|
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variable vE equal c_cKe+c_cPe
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|
||||
# specify the reservoir extents
|
||||
variable Lz equal zhi-zlo
|
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variable delta equal 4
|
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variable dz equal ${Lz}/60
|
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variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
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variable zhi_Thi equal ${zlo_Thi}+${delta}
|
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variable zlo_Tlo equal ${Lz}/4.-${delta}/2.
|
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variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
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|
||||
# create regions of low and high temperature and apply thermostats
|
||||
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}
|
||||
|
||||
# compute temperature of reservoirs using 3 degrees of freedom for every atom
|
||||
compute cTlo water temp/region Tlo_region
|
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compute cThi water temp/region Thi_region
|
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|
||||
# rescale temperature to correct for the constraint bonds (6 instead of 9 degrees of freedom per molecule)
|
||||
variable Tlo_act equal c_cTlo/2*3
|
||||
variable Thi_act equal c_cThi/2*3
|
||||
|
||||
# thermostat the reservoirs using the eHEX algorithm
|
||||
# NOTE: add the keyword "hex" at the end of each of the two following lines
|
||||
# if you want to use the HEX algorithm.
|
||||
|
||||
fix fHi all ehex 1 ${F} region Thi_region com constrain
|
||||
fix fLo all ehex 1 -${F} region Tlo_region com constrain
|
||||
|
||||
# use velocity Verlet integration
|
||||
fix fNVE all nve
|
||||
|
||||
# calculate the (kinetic) temperature from the kinetic
|
||||
# energy per atom
|
||||
# kB is Boltzmann's constant
|
||||
# NOTE: For simplicity, we do not subtract the centre of mass
|
||||
# velocity of the individual slabs in this example script.
|
||||
# However, we did take this into account in the publication.
|
||||
# (The differences are negligible for our setup.)
|
||||
|
||||
variable kB equal 0.001987204
|
||||
compute ke water ke/atom
|
||||
variable T atom c_ke/${kB}
|
||||
|
||||
# use RATTLE with a precision of 1.e-10
|
||||
fix fRattle all rattle 1e-10 400 0 b 1 a 1
|
||||
|
||||
# output the timestep, temperatures (average, cold reservoir, hot reservoir), energies (kinetic, potential and total),
|
||||
# pressure and squared com velocity every 100 timesteps
|
||||
reset_timestep 0
|
||||
timestep ${dt}
|
||||
|
||||
thermo_style custom step temp v_Tlo_act v_Thi_act ke pe etotal press v_vcm2
|
||||
thermo_modify flush yes
|
||||
thermo 1000
|
||||
|
||||
compute cchT all chunk/atom bin/1d z lower ${dz}
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_ehex
|
||||
|
||||
fix fE all ave/time 10 500 5000 v_vE file out.Espce_ehex
|
||||
run ${Nprod}
|
||||
|
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@ -0,0 +1,160 @@
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###############################################################################
|
||||
#
|
||||
#
|
||||
# This input script is a modified version of the example script spce_hex.lmp
|
||||
# which is part of the supplementary (open access) material of the paper
|
||||
#
|
||||
# P. Wirnsberger, D. Frenkel and C. Dellago,
|
||||
# "An enhanced version of the heat exchange algorithm with excellent energy
|
||||
# conservation properties", J. Chem. Phys. 143, 124104 (2015).
|
||||
#
|
||||
# The full article is available on arXiv: http://arxiv.org/pdf/1507.07081.
|
||||
#
|
||||
#
|
||||
# Description:
|
||||
# ------------
|
||||
#
|
||||
# This file is a LAMMPS input script for carrying out a NEMD simulation of
|
||||
# SPC/E water using the HEX/a algorithm. The run produces two files:
|
||||
# "out.Tspce_hex" contains the temperature profile and "out.Espce_hex" the time
|
||||
# evolution of the total energy.
|
||||
#
|
||||
###############################################################################
|
||||
|
||||
log log.spce_hex
|
||||
|
||||
# energy flux into the reservoir
|
||||
variable F equal 0.075
|
||||
|
||||
# timestep
|
||||
variable dt equal 3.0
|
||||
|
||||
# simulation time for the production run (1 ns)
|
||||
variable tprod equal 1000000
|
||||
|
||||
# total number of timesteps
|
||||
variable Nprod equal floor(${tprod}/${dt})
|
||||
|
||||
# parameters for the SPC/E model
|
||||
variable epsOO equal 0.15535
|
||||
variable sigOO equal 3.166
|
||||
variable theta equal 109.47
|
||||
|
||||
# long-range and short-range cutoffs, respectively
|
||||
variable cutC equal (xhi-xlo)/2.
|
||||
variable cutLJ equal 11
|
||||
|
||||
# specification of units, spatial dimensions, boundary conditions and atom-style
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
read_data "data.spce"
|
||||
|
||||
# group atoms to molecules
|
||||
group O type 2
|
||||
group H type 1
|
||||
group water type 1 2
|
||||
|
||||
# define the pair style with long-range Coulomb interaction
|
||||
# and short-range LJ interaction
|
||||
pair_style lj/cut/coul/long ${cutLJ} ${cutC}
|
||||
pair_coeff 2 2 ${epsOO} ${sigOO}
|
||||
pair_coeff 1 2 0 0
|
||||
pair_coeff 1 1 0 0
|
||||
|
||||
# use Ewald summation with a precision of 1.e-5
|
||||
kspace_style ewald 1.e-5
|
||||
|
||||
# use harmonic bonds between sites of a molecules
|
||||
# NOTE: this will not have any effects as we use RATTLE to keep the bonds fixed,
|
||||
# but it is recommended.
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 ${theta}
|
||||
|
||||
# use standard correction terms for the truncated tail of the LJ potential
|
||||
pair_modify tail yes
|
||||
|
||||
# increase neigbor skin because of the large timestep
|
||||
neighbor 4.5 bin
|
||||
|
||||
variable Nsamp equal 10
|
||||
variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
||||
variable Nevery equal ${Nsamp}*${Nrepeat}
|
||||
|
||||
# compute the centre of mass velocity of the 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
|
||||
|
||||
# compute temperature, pressure, potential energy, kinetic energy and total energy
|
||||
compute cT all temp
|
||||
compute cP all pressure thermo_temp
|
||||
compute cPe all pe
|
||||
compute cKe all ke
|
||||
variable vE equal c_cKe+c_cPe
|
||||
|
||||
# specify the reservoir extents
|
||||
variable Lz equal zhi-zlo
|
||||
variable delta equal 4
|
||||
variable dz equal ${Lz}/60
|
||||
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
||||
variable zhi_Thi equal ${zlo_Thi}+${delta}
|
||||
variable zlo_Tlo equal ${Lz}/4.-${delta}/2.
|
||||
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
||||
|
||||
# create regions of low and high temperature and apply thermostats
|
||||
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 temperature of reservoirs using 3 degrees of freedom for every atom
|
||||
compute cTlo water temp/region Tlo_region
|
||||
compute cThi water temp/region Thi_region
|
||||
|
||||
# rescale temperature to correct for the constraint bonds (6 instead of 9 degrees of freedom per molecule)
|
||||
variable Tlo_act equal c_cTlo/2*3
|
||||
variable Thi_act equal c_cThi/2*3
|
||||
|
||||
# thermostat the reservoirs using the eHEX algorithm
|
||||
# NOTE: add the keyword "hex" at the end of each of the two following lines
|
||||
# if you want to use the HEX algorithm.
|
||||
|
||||
fix fHi all ehex 1 ${F} region Thi_region com constrain hex
|
||||
fix fLo all ehex 1 -${F} region Tlo_region com constrain hex
|
||||
|
||||
# use velocity Verlet integration
|
||||
fix fNVE all nve
|
||||
|
||||
# calculate the (kinetic) temperature from the kinetic
|
||||
# energy per atom
|
||||
# kB is Boltzmann's constant
|
||||
# NOTE: For simplicity, we do not subtract the centre of mass
|
||||
# velocity of the individual slabs in this example script.
|
||||
# However, we did take this into account in the publication.
|
||||
# (The differences are negligible for our setup.)
|
||||
|
||||
variable kB equal 0.001987204
|
||||
compute ke water ke/atom
|
||||
variable T atom c_ke/${kB}
|
||||
|
||||
# use RATTLE with a precision of 1.e-10
|
||||
fix fRattle all rattle 1e-10 400 0 b 1 a 1
|
||||
|
||||
# output the timestep, temperatures (average, cold reservoir, hot reservoir), energies (kinetic, potential and total),
|
||||
# pressure and squared com velocity every 100 timesteps
|
||||
reset_timestep 0
|
||||
timestep ${dt}
|
||||
|
||||
thermo_style custom step temp v_Tlo_act v_Thi_act ke pe etotal press v_vcm2
|
||||
thermo_modify flush yes
|
||||
thermo 1000
|
||||
|
||||
compute cchT all chunk/atom bin/1d z lower ${dz}
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_hex
|
||||
|
||||
fix fE all ave/time 10 500 5000 v_vE file out.Espce_hex
|
||||
run ${Nprod}
|
||||
|
|
@ -0,0 +1,256 @@
|
|||
|
||||
# heat flux
|
||||
variable J equal 0.15
|
||||
|
||||
# timestep
|
||||
variable dt equal 0.007
|
||||
|
||||
# cutoff radius for shifted LJ-potential
|
||||
variable rc equal 3.0
|
||||
|
||||
# simulation time for the production run
|
||||
variable tprod equal 5000
|
||||
|
||||
# total number of timesteps
|
||||
variable Nprod equal floor(${tprod}/${dt})
|
||||
variable Nprod equal floor(5000/${dt})
|
||||
variable Nprod equal floor(5000/0.007)
|
||||
|
||||
# equilibrated steady state configuration
|
||||
read_data "data.lj"
|
||||
orthogonal box = (-5.28998 -5.28998 -10.58) to (5.28998 5.28998 10.58)
|
||||
2 by 2 by 8 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
reading velocities ...
|
||||
2000 velocities
|
||||
|
||||
# use LJ shifted force pair style
|
||||
pair_style lj/sf ${rc}
|
||||
pair_style lj/sf 3
|
||||
|
||||
# with coefficients eps = 1, sigma = 1, and rc = 3.0
|
||||
pair_coeff 1 1 1.0 1.0 ${rc}
|
||||
pair_coeff 1 1 1.0 1.0 3
|
||||
|
||||
# increase neigbor skin because of the large timestep
|
||||
neighbor 0.8 bin
|
||||
|
||||
# options used for fix ave/time; sample the quantities every 10 steps
|
||||
variable Nsamp equal 10
|
||||
variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
||||
variable Nrepeat equal floor(714285/${Nsamp})
|
||||
variable Nrepeat equal floor(714285/10)
|
||||
variable Nevery equal ${Nsamp}*${Nrepeat}
|
||||
variable Nevery equal 10*${Nrepeat}
|
||||
variable Nevery equal 10*71428
|
||||
|
||||
# box dimensions
|
||||
variable Lz equal zhi-zlo
|
||||
variable Lx equal xhi-xlo
|
||||
variable Ly equal yhi-ylo
|
||||
|
||||
# reservoir width in z-direction
|
||||
variable delta equal 2.
|
||||
|
||||
# specify z-extents of both reservoirs
|
||||
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
||||
variable zlo_Thi equal -21.16/4.-${delta}/2.
|
||||
variable zlo_Thi equal -21.16/4.-2/2.
|
||||
variable zhi_Thi equal ${zlo_Thi}+${delta}
|
||||
variable zhi_Thi equal -6.29+${delta}
|
||||
variable zhi_Thi equal -6.29+2
|
||||
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
|
||||
variable zlo_Tlo equal -6.29+${Lz}/2.
|
||||
variable zlo_Tlo equal -6.29+21.16/2.
|
||||
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
||||
variable zhi_Tlo equal 4.29+${delta}
|
||||
variable zhi_Tlo equal 4.29+2
|
||||
|
||||
# resolution for fix ave/spatial
|
||||
variable dz equal ${Lz}/60
|
||||
variable dz equal 21.16/60
|
||||
|
||||
# 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 Thi_region block INF INF INF INF -6.29 ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -6.29 -4.29
|
||||
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 4.29 ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 4.29 6.29
|
||||
|
||||
# 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}*${Ly}*2.
|
||||
variable F equal 0.15*${Lx}*${Ly}*2.
|
||||
variable F equal 0.15*10.57996*${Ly}*2.
|
||||
variable F equal 0.15*10.57996*10.57996*2.
|
||||
|
||||
# use fix ehex to create the gradient
|
||||
# hot reservoir
|
||||
fix fHi all ehex 1 +${F} region Thi_region
|
||||
fix fHi all ehex 1 +33.58066608048 region Thi_region
|
||||
|
||||
# cold reservoir
|
||||
fix fLo all ehex 1 -${F} region Tlo_region
|
||||
fix fLo all ehex 1 -33.58066608048 region Tlo_region
|
||||
|
||||
# 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}
|
||||
timestep 0.007
|
||||
|
||||
# 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}
|
||||
compute cchT all chunk/atom bin/1d z lower 0.352666666666667
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_ehex
|
||||
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_ehex
|
||||
fix fchT all ave/chunk 10 71428 ${Nevery} cchT v_T file out.Tlj_ehex
|
||||
fix fchT all ave/chunk 10 71428 714280 cchT v_T file out.Tlj_ehex
|
||||
|
||||
# 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_ehex
|
||||
fix fE all ave/time 10 1000 10000 v_E file out.Elj_ehex
|
||||
|
||||
# production run
|
||||
run ${Nprod}
|
||||
run 714285
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 1.9 -> bins = 6 6 12
|
||||
Memory usage per processor = 2.40563 Mbytes
|
||||
Step Temp TotEng vcm2
|
||||
0 0.72367949 -4.1076054 7.0171467e-30
|
||||
10000 0.72399955 -4.1075876 6.3569796e-30
|
||||
20000 0.72200145 -4.1076527 9.4131743e-30
|
||||
30000 0.7189538 -4.1076266 9.9917978e-30
|
||||
40000 0.72493542 -4.1075882 1.2907194e-29
|
||||
50000 0.71651186 -4.1076193 1.6114353e-29
|
||||
60000 0.73095328 -4.107638 1.6281247e-29
|
||||
70000 0.70276229 -4.1074716 1.5732538e-29
|
||||
80000 0.71186017 -4.1075456 1.9714873e-29
|
||||
90000 0.7277987 -4.1076333 1.9683783e-29
|
||||
100000 0.74378417 -4.1076831 2.008245e-29
|
||||
110000 0.7066978 -4.1074049 1.8623846e-29
|
||||
120000 0.72500229 -4.1075844 2.117713e-29
|
||||
130000 0.72008927 -4.1076012 2.3931505e-29
|
||||
140000 0.72772233 -4.1076511 2.1582564e-29
|
||||
150000 0.73860983 -4.1077211 2.4705578e-29
|
||||
160000 0.72961264 -4.1074785 2.7170029e-29
|
||||
170000 0.71734552 -4.1074323 2.4675122e-29
|
||||
180000 0.70571153 -4.1074453 2.2384488e-29
|
||||
190000 0.72598398 -4.1076489 2.6149518e-29
|
||||
200000 0.71654285 -4.1075445 2.2884041e-29
|
||||
210000 0.70521682 -4.1075104 2.1544528e-29
|
||||
220000 0.72901276 -4.107639 2.2758013e-29
|
||||
230000 0.73245466 -4.1075811 2.4878827e-29
|
||||
240000 0.71163454 -4.1074882 2.072386e-29
|
||||
250000 0.72347298 -4.1075939 2.0114174e-29
|
||||
260000 0.71577745 -4.1075268 1.8020948e-29
|
||||
270000 0.71563876 -4.1075331 1.726083e-29
|
||||
280000 0.71472187 -4.1076037 1.5702905e-29
|
||||
290000 0.71640897 -4.1075095 1.3652432e-29
|
||||
300000 0.71189676 -4.1074701 1.3273904e-29
|
||||
310000 0.73110074 -4.1075712 1.2920349e-29
|
||||
320000 0.73650669 -4.107631 1.3923757e-29
|
||||
330000 0.69674914 -4.1074138 1.4152976e-29
|
||||
340000 0.72631298 -4.1077512 1.386547e-29
|
||||
350000 0.72730004 -4.1077609 1.6375273e-29
|
||||
360000 0.73133088 -4.1076599 1.4915012e-29
|
||||
370000 0.71990302 -4.1075023 1.4387132e-29
|
||||
380000 0.70764996 -4.1075914 1.4723241e-29
|
||||
390000 0.7255125 -4.1077323 1.6664958e-29
|
||||
400000 0.7326785 -4.1077028 1.5203345e-29
|
||||
410000 0.71953373 -4.1075658 2.0232789e-29
|
||||
420000 0.71143005 -4.107548 2.229431e-29
|
||||
430000 0.74033148 -4.1076115 2.657992e-29
|
||||
440000 0.7267839 -4.1077112 2.9458629e-29
|
||||
450000 0.71505305 -4.107557 2.9103833e-29
|
||||
460000 0.7089713 -4.1075146 3.3253897e-29
|
||||
470000 0.72444212 -4.1076379 3.1465484e-29
|
||||
480000 0.72079711 -4.1075868 2.8388782e-29
|
||||
490000 0.71267656 -4.1074868 3.2128913e-29
|
||||
500000 0.70974489 -4.1076207 3.5271604e-29
|
||||
510000 0.7053828 -4.1074928 3.7845378e-29
|
||||
520000 0.71396356 -4.107609 3.520462e-29
|
||||
530000 0.71637729 -4.1075377 3.131853e-29
|
||||
540000 0.72648522 -4.1075216 2.9893315e-29
|
||||
550000 0.7012357 -4.1074612 2.9823982e-29
|
||||
560000 0.71040667 -4.1074729 2.9340227e-29
|
||||
570000 0.73041709 -4.1074866 3.398074e-29
|
||||
580000 0.71814185 -4.107633 3.4865255e-29
|
||||
590000 0.72128126 -4.1074578 3.6128155e-29
|
||||
600000 0.72342897 -4.107554 3.1929655e-29
|
||||
610000 0.71695081 -4.1075492 3.110134e-29
|
||||
620000 0.7144036 -4.1076465 3.734556e-29
|
||||
630000 0.74624251 -4.1076366 3.9372399e-29
|
||||
640000 0.72448733 -4.1076427 4.0683832e-29
|
||||
650000 0.71347763 -4.1075844 4.2153755e-29
|
||||
660000 0.72287745 -4.1075678 4.3130586e-29
|
||||
670000 0.71618749 -4.1075379 4.1023799e-29
|
||||
680000 0.71846662 -4.1075145 4.0775831e-29
|
||||
690000 0.72276205 -4.1076277 4.6351083e-29
|
||||
700000 0.71712649 -4.1077598 4.6374261e-29
|
||||
710000 0.71280668 -4.1074476 4.8082341e-29
|
||||
714285 0.72291151 -4.1075743 4.8273006e-29
|
||||
Loop time of 170.968 on 32 procs for 714285 steps with 2000 atoms
|
||||
|
||||
Performance: 2526790.532 tau/day, 4177.894 timesteps/s
|
||||
100.0% CPU use with 32 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 68.213 | 77.684 | 85.031 | 57.6 | 45.44
|
||||
Neigh | 8.8658 | 9.609 | 10.196 | 14.8 | 5.62
|
||||
Comm | 49.931 | 56.883 | 67.495 | 60.5 | 33.27
|
||||
Output | 0.013727 | 0.014771 | 0.014943 | 0.2 | 0.01
|
||||
Modify | 20.448 | 22.358 | 25.099 | 32.3 | 13.08
|
||||
Other | | 4.419 | | | 2.58
|
||||
|
||||
Nlocal: 62.5 ave 69 max 55 min
|
||||
Histogram: 2 1 3 5 3 4 2 8 2 2
|
||||
Nghost: 1371 ave 1405 max 1338 min
|
||||
Histogram: 2 4 6 4 0 3 4 3 1 5
|
||||
Neighs: 6007.94 ave 6893 max 5323 min
|
||||
Histogram: 4 6 3 3 5 2 1 2 2 4
|
||||
|
||||
Total # of neighbors = 192254
|
||||
Ave neighs/atom = 96.127
|
||||
Neighbor list builds = 40326
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:02:50
|
|
@ -0,0 +1,256 @@
|
|||
|
||||
# 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}/${dt})
|
||||
variable Nprod equal floor(5000/${dt})
|
||||
variable Nprod equal floor(5000/0.007)
|
||||
|
||||
# equilibrated steady state configuration
|
||||
read_data "data.lj"
|
||||
orthogonal box = (-5.28998 -5.28998 -10.58) to (5.28998 5.28998 10.58)
|
||||
2 by 2 by 8 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
reading velocities ...
|
||||
2000 velocities
|
||||
|
||||
# use LJ shifted force pair style
|
||||
pair_style lj/sf ${rc}
|
||||
pair_style lj/sf 3
|
||||
|
||||
# with coefficients eps = 1, sigma = 1, and rc = 3.0
|
||||
pair_coeff 1 1 1.0 1.0 ${rc}
|
||||
pair_coeff 1 1 1.0 1.0 3
|
||||
|
||||
# increase neigbor skin because of the large timestep
|
||||
neighbor 0.8 bin
|
||||
|
||||
# options used for fix ave/time; sample the quantities every 10 steps
|
||||
variable Nsamp equal 10
|
||||
variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
||||
variable Nrepeat equal floor(714285/${Nsamp})
|
||||
variable Nrepeat equal floor(714285/10)
|
||||
variable Nevery equal ${Nsamp}*${Nrepeat}
|
||||
variable Nevery equal 10*${Nrepeat}
|
||||
variable Nevery equal 10*71428
|
||||
|
||||
# box dimensions
|
||||
variable Lz equal zhi-zlo
|
||||
variable Lx equal xhi-xlo
|
||||
variable Ly equal yhi-ylo
|
||||
|
||||
# reservoir width in z-direction
|
||||
variable delta equal 2.
|
||||
|
||||
# specify z-extents of both reservoirs
|
||||
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
||||
variable zlo_Thi equal -21.16/4.-${delta}/2.
|
||||
variable zlo_Thi equal -21.16/4.-2/2.
|
||||
variable zhi_Thi equal ${zlo_Thi}+${delta}
|
||||
variable zhi_Thi equal -6.29+${delta}
|
||||
variable zhi_Thi equal -6.29+2
|
||||
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
|
||||
variable zlo_Tlo equal -6.29+${Lz}/2.
|
||||
variable zlo_Tlo equal -6.29+21.16/2.
|
||||
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
||||
variable zhi_Tlo equal 4.29+${delta}
|
||||
variable zhi_Tlo equal 4.29+2
|
||||
|
||||
# resolution for fix ave/spatial
|
||||
variable dz equal ${Lz}/60
|
||||
variable dz equal 21.16/60
|
||||
|
||||
# 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 Thi_region block INF INF INF INF -6.29 ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -6.29 -4.29
|
||||
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 4.29 ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 4.29 6.29
|
||||
|
||||
# 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}*${Ly}*2.
|
||||
variable F equal 0.15*${Lx}*${Ly}*2.
|
||||
variable F equal 0.15*10.57996*${Ly}*2.
|
||||
variable F equal 0.15*10.57996*10.57996*2.
|
||||
|
||||
# use fix ehex to create the gradient
|
||||
# hot reservoir
|
||||
fix fHi all ehex 1 +${F} region Thi_region hex
|
||||
fix fHi all ehex 1 +33.58066608048 region Thi_region hex
|
||||
|
||||
# cold reservoir
|
||||
fix fLo all ehex 1 -${F} region Tlo_region hex
|
||||
fix fLo all ehex 1 -33.58066608048 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}
|
||||
timestep 0.007
|
||||
|
||||
# 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}
|
||||
compute cchT all chunk/atom bin/1d z lower 0.352666666666667
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
|
||||
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
|
||||
fix fchT all ave/chunk 10 71428 ${Nevery} cchT v_T file out.Tlj_hex
|
||||
fix fchT all ave/chunk 10 71428 714280 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
|
||||
fix fE all ave/time 10 1000 10000 v_E file out.Elj_hex
|
||||
|
||||
# production run
|
||||
run ${Nprod}
|
||||
run 714285
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 1.9 -> bins = 6 6 12
|
||||
Memory usage per processor = 2.40563 Mbytes
|
||||
Step Temp TotEng vcm2
|
||||
0 0.72367949 -4.1076054 7.0171467e-30
|
||||
10000 0.71696731 -4.1078382 1.1938548e-29
|
||||
20000 0.71725882 -4.1080333 1.5504952e-29
|
||||
30000 0.7228273 -4.1083683 1.403949e-29
|
||||
40000 0.73478918 -4.1087812 1.446699e-29
|
||||
50000 0.72841192 -4.1089089 1.3198991e-29
|
||||
60000 0.74581896 -4.1093422 1.5059838e-29
|
||||
70000 0.72063371 -4.109324 1.6171041e-29
|
||||
80000 0.72009466 -4.1095719 1.6870537e-29
|
||||
90000 0.73014429 -4.109994 1.571385e-29
|
||||
100000 0.71327476 -4.1101323 1.5412564e-29
|
||||
110000 0.72316493 -4.1104409 1.7709502e-29
|
||||
120000 0.7234872 -4.1105344 1.7948787e-29
|
||||
130000 0.72816899 -4.1109221 1.7741547e-29
|
||||
140000 0.72506096 -4.1111987 1.9030371e-29
|
||||
150000 0.72511673 -4.1114823 1.757343e-29
|
||||
160000 0.73317551 -4.1116909 1.8994729e-29
|
||||
170000 0.72082439 -4.1120083 1.865766e-29
|
||||
180000 0.72626999 -4.112335 1.9148683e-29
|
||||
190000 0.71326654 -4.1124685 1.8915793e-29
|
||||
200000 0.74065832 -4.112821 1.9843217e-29
|
||||
210000 0.71845086 -4.1131127 2.4402147e-29
|
||||
220000 0.71791233 -4.1132362 2.2097117e-29
|
||||
230000 0.7208125 -4.1135103 2.4606119e-29
|
||||
240000 0.72909134 -4.1136773 2.2783022e-29
|
||||
250000 0.71684431 -4.1140752 2.1670987e-29
|
||||
260000 0.72213406 -4.1143319 1.8390834e-29
|
||||
270000 0.72455866 -4.1146051 1.5318237e-29
|
||||
280000 0.73251834 -4.114923 1.6228615e-29
|
||||
290000 0.72332528 -4.1150291 1.8472989e-29
|
||||
300000 0.72197256 -4.1153626 1.8294525e-29
|
||||
310000 0.71912916 -4.1155306 1.6031831e-29
|
||||
320000 0.71457342 -4.1158131 1.7531014e-29
|
||||
330000 0.72421737 -4.1161772 1.9968319e-29
|
||||
340000 0.72235101 -4.1163113 2.3190719e-29
|
||||
350000 0.70988998 -4.1164748 2.5611335e-29
|
||||
360000 0.71775456 -4.1169932 3.0014053e-29
|
||||
370000 0.71679741 -4.1170966 3.0945259e-29
|
||||
380000 0.70612966 -4.117342 2.9062249e-29
|
||||
390000 0.70739305 -4.1177322 2.7053082e-29
|
||||
400000 0.71295005 -4.1179697 2.4414341e-29
|
||||
410000 0.72470924 -4.118195 2.1651938e-29
|
||||
420000 0.70443619 -4.1186353 1.876675e-29
|
||||
430000 0.72845824 -4.1189494 1.6850186e-29
|
||||
440000 0.71062175 -4.119168 1.3962175e-29
|
||||
450000 0.71550284 -4.1192887 1.9906124e-29
|
||||
460000 0.71447701 -4.1196143 1.6312135e-29
|
||||
470000 0.71361306 -4.1197326 1.5080229e-29
|
||||
480000 0.72704141 -4.1202699 1.6559898e-29
|
||||
490000 0.72221343 -4.1203799 1.582088e-29
|
||||
500000 0.71244432 -4.1206248 1.1449744e-29
|
||||
510000 0.70019538 -4.1208159 9.6577977e-30
|
||||
520000 0.7093834 -4.1210854 9.2916455e-30
|
||||
530000 0.71987196 -4.1213538 9.1536296e-30
|
||||
540000 0.71955704 -4.121897 8.9426037e-30
|
||||
550000 0.72739215 -4.1219256 7.885467e-30
|
||||
560000 0.70927863 -4.122129 6.8477877e-30
|
||||
570000 0.70617194 -4.1224777 5.700215e-30
|
||||
580000 0.71925255 -4.1227138 5.5056496e-30
|
||||
590000 0.71501495 -4.1230402 5.273532e-30
|
||||
600000 0.71662363 -4.1233293 3.9763449e-30
|
||||
610000 0.71711036 -4.123687 3.1692329e-30
|
||||
620000 0.72296651 -4.1240099 2.4431085e-30
|
||||
630000 0.71994644 -4.1240367 1.9069135e-30
|
||||
640000 0.7086421 -4.1243122 1.5270107e-30
|
||||
650000 0.70878259 -4.1245389 2.9144979e-30
|
||||
660000 0.70731638 -4.1247635 3.1199575e-30
|
||||
670000 0.7218969 -4.1252117 2.306873e-30
|
||||
680000 0.71825558 -4.1254141 1.085262e-30
|
||||
690000 0.71399204 -4.1256692 1.5706617e-30
|
||||
700000 0.72094628 -4.1259655 2.058912e-30
|
||||
710000 0.70106365 -4.1262688 3.8784102e-30
|
||||
714285 0.70771156 -4.1262914 4.2318798e-30
|
||||
Loop time of 170.167 on 32 procs for 714285 steps with 2000 atoms
|
||||
|
||||
Performance: 2538674.602 tau/day, 4197.544 timesteps/s
|
||||
100.0% CPU use with 32 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 69.016 | 77.498 | 85.354 | 57.0 | 45.54
|
||||
Neigh | 8.8368 | 9.5809 | 10.199 | 15.2 | 5.63
|
||||
Comm | 49.229 | 56.994 | 66.176 | 59.6 | 33.49
|
||||
Output | 0.013675 | 0.014766 | 0.014929 | 0.2 | 0.01
|
||||
Modify | 19.558 | 21.817 | 24.56 | 35.3 | 12.82
|
||||
Other | | 4.263 | | | 2.51
|
||||
|
||||
Nlocal: 62.5 ave 71 max 54 min
|
||||
Histogram: 2 0 4 3 7 7 2 5 1 1
|
||||
Nghost: 1381.91 ave 1426 max 1343 min
|
||||
Histogram: 3 6 2 4 1 3 6 1 3 3
|
||||
Neighs: 6004.25 ave 6872 max 5037 min
|
||||
Histogram: 3 1 3 6 1 5 2 4 4 3
|
||||
|
||||
Total # of neighbors = 192136
|
||||
Ave neighs/atom = 96.068
|
||||
Neighbor list builds = 40221
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:02:50
|
|
@ -0,0 +1,574 @@
|
|||
|
||||
# energy flux into the reservoir
|
||||
variable F equal 0.075
|
||||
|
||||
# timestep
|
||||
variable dt equal 3.0
|
||||
|
||||
# simulation time for the production run (1 ns)
|
||||
variable tprod equal 1000000
|
||||
|
||||
# total number of timesteps
|
||||
variable Nprod equal floor(${tprod}/${dt})
|
||||
variable Nprod equal floor(1000000/${dt})
|
||||
variable Nprod equal floor(1000000/3)
|
||||
|
||||
# parameters for the SPC/E model
|
||||
variable epsOO equal 0.15535
|
||||
variable sigOO equal 3.166
|
||||
variable theta equal 109.47
|
||||
|
||||
# long-range and short-range cutoffs, respectively
|
||||
variable cutC equal (xhi-xlo)/2.
|
||||
variable cutLJ equal 11
|
||||
|
||||
# specification of units, spatial dimensions, boundary conditions and atom-style
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
read_data "data.spce"
|
||||
orthogonal box = (-12.6314 -12.6314 -25.2628) to (12.6314 12.6314 25.2628)
|
||||
2 by 4 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
3072 atoms
|
||||
reading velocities ...
|
||||
3072 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2048 bonds
|
||||
reading angles ...
|
||||
1024 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# group atoms to molecules
|
||||
group O type 2
|
||||
1024 atoms in group O
|
||||
group H type 1
|
||||
2048 atoms in group H
|
||||
group water type 1 2
|
||||
3072 atoms in group water
|
||||
|
||||
# define the pair style with long-range Coulomb interaction
|
||||
# and short-range LJ interaction
|
||||
pair_style lj/cut/coul/long ${cutLJ} ${cutC}
|
||||
pair_style lj/cut/coul/long 11 ${cutC}
|
||||
pair_style lj/cut/coul/long 11 12.6314
|
||||
pair_coeff 2 2 ${epsOO} ${sigOO}
|
||||
pair_coeff 2 2 0.15535 ${sigOO}
|
||||
pair_coeff 2 2 0.15535 3.166
|
||||
pair_coeff 1 2 0 0
|
||||
pair_coeff 1 1 0 0
|
||||
|
||||
# use Ewald summation with a precision of 1.e-5
|
||||
kspace_style ewald 1.e-5
|
||||
|
||||
# use harmonic bonds between sites of a molecules
|
||||
# NOTE: this will not have any effects as we use RATTLE to keep the bonds fixed,
|
||||
# but it is recommended.
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 ${theta}
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
# increase neigbor skin because of the large timestep
|
||||
neighbor 4.5 bin
|
||||
|
||||
# use standard correction terms for the truncated tail of the LJ potential
|
||||
pair_modify tail yes
|
||||
|
||||
variable Nsamp equal 10
|
||||
variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
||||
variable Nrepeat equal floor(333333/${Nsamp})
|
||||
variable Nrepeat equal floor(333333/10)
|
||||
variable Nevery equal ${Nsamp}*${Nrepeat}
|
||||
variable Nevery equal 10*${Nrepeat}
|
||||
variable Nevery equal 10*33333
|
||||
|
||||
# compute the centre of mass velocity of the 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
|
||||
|
||||
# compute temperature, pressure, potential energy, kinetic energy and total energy
|
||||
compute cT all temp
|
||||
compute cP all pressure thermo_temp
|
||||
compute cPe all pe
|
||||
compute cKe all ke
|
||||
variable vE equal c_cKe+c_cPe
|
||||
|
||||
# specify the reservoir extents
|
||||
variable Lz equal zhi-zlo
|
||||
variable delta equal 4
|
||||
variable dz equal ${Lz}/60
|
||||
variable dz equal 50.5255/60
|
||||
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
||||
variable zlo_Thi equal -50.5255/4.-${delta}/2.
|
||||
variable zlo_Thi equal -50.5255/4.-4/2.
|
||||
variable zhi_Thi equal ${zlo_Thi}+${delta}
|
||||
variable zhi_Thi equal -14.631375+${delta}
|
||||
variable zhi_Thi equal -14.631375+4
|
||||
variable zlo_Tlo equal ${Lz}/4.-${delta}/2.
|
||||
variable zlo_Tlo equal 50.5255/4.-${delta}/2.
|
||||
variable zlo_Tlo equal 50.5255/4.-4/2.
|
||||
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
||||
variable zhi_Tlo equal 10.631375+${delta}
|
||||
variable zhi_Tlo equal 10.631375+4
|
||||
|
||||
# create regions of low and high temperature and apply thermostats
|
||||
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -14.631375 ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -14.631375 -10.631375
|
||||
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 10.631375 ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 10.631375 14.631375
|
||||
|
||||
# compute temperature of reservoirs using 3 degrees of freedom for every atom
|
||||
compute cTlo water temp/region Tlo_region
|
||||
compute cThi water temp/region Thi_region
|
||||
|
||||
# rescale temperature to correct for the constraint bonds (6 instead of 9 degrees of freedom per molecule)
|
||||
variable Tlo_act equal c_cTlo/2*3
|
||||
variable Thi_act equal c_cThi/2*3
|
||||
|
||||
# thermostat the reservoirs using the eHEX algorithm
|
||||
# NOTE: add the keyword "hex" at the end of each of the two following lines
|
||||
# if you want to use the HEX algorithm.
|
||||
|
||||
fix fHi all ehex 1 ${F} region Thi_region com constrain
|
||||
fix fHi all ehex 1 0.075 region Thi_region com constrain
|
||||
fix fLo all ehex 1 -${F} region Tlo_region com constrain
|
||||
fix fLo all ehex 1 -0.075 region Tlo_region com constrain
|
||||
|
||||
# use velocity Verlet integration
|
||||
fix fNVE all nve
|
||||
|
||||
# calculate the (kinetic) temperature from the kinetic
|
||||
# energy per atom
|
||||
# kB is Boltzmann's constant
|
||||
# NOTE: For simplicity, we do not subtract the centre of mass
|
||||
# velocity of the individual slabs in this example script.
|
||||
# However, we did take this into account in the publication.
|
||||
# (The differences are negligible for our setup.)
|
||||
|
||||
variable kB equal 0.001987204
|
||||
compute ke water ke/atom
|
||||
variable T atom c_ke/${kB}
|
||||
variable T atom c_ke/0.001987204
|
||||
|
||||
# use RATTLE with a precision of 1.e-10
|
||||
fix fRattle all rattle 1e-10 400 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1024 = # of frozen angles
|
||||
|
||||
# output the timestep, temperatures (average, cold reservoir, hot reservoir), energies (kinetic, potential and total),
|
||||
# pressure and squared com velocity every 100 timesteps
|
||||
reset_timestep 0
|
||||
timestep ${dt}
|
||||
timestep 3
|
||||
|
||||
thermo_style custom step temp v_Tlo_act v_Thi_act ke pe etotal press v_vcm2
|
||||
thermo_modify flush yes
|
||||
thermo 1000
|
||||
|
||||
compute cchT all chunk/atom bin/1d z lower ${dz}
|
||||
compute cchT all chunk/atom bin/1d z lower 0.842091666666667
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_ehex
|
||||
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_ehex
|
||||
fix fchT all ave/chunk 10 33333 ${Nevery} cchT v_T file out.Tspce_ehex
|
||||
fix fchT all ave/chunk 10 33333 333330 cchT v_T file out.Tspce_ehex
|
||||
|
||||
fix fE all ave/time 10 500 5000 v_vE file out.Espce_ehex
|
||||
run ${Nprod}
|
||||
run 333333
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.234029
|
||||
estimated absolute RMS force accuracy = 0.00363217
|
||||
estimated relative force accuracy = 1.09382e-05
|
||||
KSpace vectors: actual max1d max3d = 903 11 6083
|
||||
kxmax kymax kzmax = 6 6 11
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.1314
|
||||
ghost atom cutoff = 17.1314
|
||||
binsize = 8.5657 -> bins = 3 3 6
|
||||
Memory usage per processor = 8.42898 Mbytes
|
||||
Step Temp Tlo_act Thi_act KinEng PotEng TotEng Press vcm2
|
||||
0 399.28553 345.31026 514.38426 2436.3278 -10062.57 -7626.2426 316.77546 8.2636936e-24
|
||||
1000 399.6682 350.66492 518.51571 2438.6627 -10064.857 -7626.1945 810.53354 8.3674222e-24
|
||||
2000 396.4779 339.3864 407.97272 2419.1964 -10044.579 -7625.3825 460.55061 8.0803372e-24
|
||||
3000 395.92531 330.6446 448.97382 2415.8247 -10041.36 -7625.5351 463.38456 8.1595614e-24
|
||||
4000 409.17516 360.38407 463.71534 2496.6715 -10123.152 -7626.4802 1102.238 8.2702223e-24
|
||||
5000 400.53481 368.14838 495.34136 2443.9505 -10071.338 -7627.3871 459.34194 8.2783341e-24
|
||||
6000 398.97908 332.58923 492.80059 2434.4579 -10060.859 -7626.4014 54.132686 8.3068063e-24
|
||||
7000 400.47957 338.32769 446.54739 2443.6135 -10069.419 -7625.8058 486.51352 8.1855175e-24
|
||||
8000 387.79946 329.78505 426.39032 2366.243 -9991.5798 -7625.3368 122.09668 8.195384e-24
|
||||
9000 405.40434 357.36778 488.18636 2473.663 -10099.409 -7625.746 369.18523 7.9704648e-24
|
||||
10000 400.15215 363.426 462.54315 2441.6157 -10067.313 -7625.6977 139.29474 7.6478681e-24
|
||||
11000 399.14925 337.7552 508.06841 2435.4962 -10060.746 -7625.2493 418.10063 7.6346817e-24
|
||||
12000 393.84637 373.28607 458.46909 2403.1396 -10028.174 -7625.0348 1041.5395 7.7409609e-24
|
||||
13000 396.82077 302.85657 457.76724 2421.2885 -10047.984 -7626.6954 1305.9164 7.6835847e-24
|
||||
14000 401.45642 365.01054 495.21712 2449.5739 -10075.933 -7626.3591 526.97968 7.5104131e-24
|
||||
15000 401.69507 341.91785 427.17725 2451.0301 -10076.876 -7625.8455 415.64129 7.6870869e-24
|
||||
16000 399.06777 313.71421 490.04511 2434.999 -10060.503 -7625.5037 797.76607 7.6917718e-24
|
||||
17000 401.35793 346.26296 472.48763 2448.9729 -10075.523 -7626.5505 56.041203 7.4420754e-24
|
||||
18000 401.17586 361.74344 436.22786 2447.862 -10073.98 -7626.1182 1253.8589 7.6399755e-24
|
||||
19000 400.86775 340.3354 461.90185 2445.9821 -10072.14 -7626.1576 19.322007 7.6407385e-24
|
||||
20000 403.04183 373.78668 461.63844 2459.2477 -10086.03 -7626.7821 855.50585 7.4405054e-24
|
||||
21000 407.13073 321.2654 482.55205 2484.197 -10110.973 -7626.7758 784.67746 7.4229952e-24
|
||||
22000 395.49224 320.26036 477.02015 2413.1822 -10037.919 -7624.7372 136.66943 7.0700737e-24
|
||||
23000 390.70367 330.46361 466.6239 2383.9637 -10009.159 -7625.195 569.45273 6.8462516e-24
|
||||
24000 398.94315 331.51966 525.57944 2434.2386 -10060.396 -7626.1569 -335.49299 6.9410859e-24
|
||||
25000 396.34735 323.8741 454.05214 2418.3998 -10044.638 -7626.238 356.85221 7.2332687e-24
|
||||
26000 403.26348 329.59619 494.70221 2460.6001 -10087.282 -7626.6818 449.98659 7.0196976e-24
|
||||
27000 395.97368 350.64775 454.65795 2416.1198 -10042.005 -7625.8852 870.94348 6.9121724e-24
|
||||
28000 398.75695 329.9947 445.39014 2433.1025 -10059.388 -7626.2852 499.29574 6.9403516e-24
|
||||
29000 401.1849 371.44607 445.48491 2447.9172 -10074.335 -7626.418 988.6286 6.9281631e-24
|
||||
30000 393.56112 345.46687 452.42406 2401.399 -10026.981 -7625.5818 787.66489 6.6703134e-24
|
||||
31000 398.55796 331.55113 487.85189 2431.8884 -10057.529 -7625.641 166.32327 6.6689185e-24
|
||||
32000 403.4613 349.79884 477.53639 2461.8072 -10089.14 -7627.3331 1141.2975 7.0117113e-24
|
||||
33000 414.21458 362.00189 505.64621 2527.4206 -10154.836 -7627.4151 1403.6786 7.0159013e-24
|
||||
34000 401.44706 340.92014 445.76959 2449.5168 -10075.942 -7626.4249 627.52806 7.2180204e-24
|
||||
35000 385.74819 335.32102 434.24611 2353.7267 -9978.0337 -7624.307 635.54437 7.5638984e-24
|
||||
36000 405.10601 361.69158 464.92937 2471.8427 -10097.819 -7625.9764 553.32332 7.7141469e-24
|
||||
37000 397.76375 341.8547 459.88862 2427.0423 -10052.632 -7625.59 269.24637 7.8741055e-24
|
||||
38000 398.96174 337.60111 456.18721 2434.3521 -10060.2 -7625.8478 174.85985 8.1286051e-24
|
||||
39000 393.82479 352.37463 450.25909 2403.0079 -10029.213 -7626.2049 1187.4008 8.672361e-24
|
||||
40000 400.36675 348.9358 460.46364 2442.925 -10068.41 -7625.4851 485.07168 8.6522759e-24
|
||||
41000 403.36947 358.51928 449.57887 2461.2468 -10087.033 -7625.7858 871.96877 8.729163e-24
|
||||
42000 388.31358 342.69773 442.64189 2369.38 -9993.6819 -7624.3018 636.95092 8.9132525e-24
|
||||
43000 395.17098 293.65068 452.82274 2411.2219 -10036.563 -7625.3412 564.05424 8.5574528e-24
|
||||
44000 399.64727 355.81869 524.22619 2438.535 -10063.993 -7625.4584 757.70978 8.0806055e-24
|
||||
45000 395.51996 324.71217 413.66421 2413.3513 -10038.06 -7624.7091 863.77464 8.025094e-24
|
||||
46000 391.32666 313.75152 480.26208 2387.765 -10013.325 -7625.5597 399.83894 8.413524e-24
|
||||
47000 400.76129 348.15878 443.3583 2445.3324 -10071.092 -7625.76 611.597 7.9488856e-24
|
||||
48000 409.06205 344.05555 458.92887 2495.9813 -10121.841 -7625.8594 257.58313 7.8961787e-24
|
||||
49000 407.43818 367.66261 489.07563 2486.0729 -10112.645 -7626.5723 474.21049 7.8853668e-24
|
||||
50000 396.18008 321.97001 499.99213 2417.3792 -10043.143 -7625.7636 366.37899 7.8325352e-24
|
||||
51000 408.9032 308.34332 442.79502 2495.0121 -10121.953 -7626.9406 241.38519 7.8928693e-24
|
||||
52000 394.92404 354.1587 434.20561 2409.7152 -10035.345 -7625.63 304.23364 7.7944689e-24
|
||||
53000 400.67392 345.66982 479.02455 2444.7993 -10070.352 -7625.5526 490.4518 8.2911037e-24
|
||||
54000 396.58892 325.71159 469.32755 2419.8738 -10046.126 -7626.2526 768.74413 8.0366039e-24
|
||||
55000 397.45024 360.57296 412.106 2425.1293 -10049.726 -7624.5971 -53.271271 7.7044426e-24
|
||||
56000 391.8861 371.26965 471.73021 2391.1785 -10016.727 -7625.5485 856.92443 7.2756758e-24
|
||||
57000 407.99884 335.86624 526.17846 2489.4939 -10116.291 -7626.7969 542.58751 7.136995e-24
|
||||
58000 389.28281 332.40431 446.65683 2375.294 -10000.569 -7625.275 552.77599 6.6918796e-24
|
||||
59000 396.14751 329.02753 490.83097 2417.1804 -10043.111 -7625.9308 1873.7076 7.0884545e-24
|
||||
60000 400.48388 341.53138 469.88289 2443.6398 -10069.849 -7626.2097 866.78751 7.0077385e-24
|
||||
61000 405.0529 360.40811 473.42837 2471.5186 -10098.085 -7626.5659 589.56864 7.2801999e-24
|
||||
62000 402.80944 352.88699 458.8553 2457.8297 -10083.512 -7625.6821 931.53288 7.5975659e-24
|
||||
63000 394.23154 365.89877 465.63434 2405.4897 -10030.388 -7624.8987 495.71886 7.5605967e-24
|
||||
64000 402.70172 356.36226 483.96143 2457.1724 -10082.705 -7625.5326 652.6968 7.4810218e-24
|
||||
65000 405.83402 372.15033 466.22488 2476.2848 -10102.939 -7626.6539 707.4654 7.4770847e-24
|
||||
66000 402.83249 364.55904 429.24075 2457.9703 -10084.476 -7626.5061 189.74867 7.5223812e-24
|
||||
67000 393.86151 356.7876 508.87718 2403.2319 -10028.311 -7625.0792 619.40063 7.2162359e-24
|
||||
68000 394.04597 337.63039 477.20695 2404.3575 -10030.134 -7625.7766 370.54724 7.1200229e-24
|
||||
69000 395.43022 365.07574 441.40661 2412.8037 -10039.307 -7626.5032 71.843512 7.3605622e-24
|
||||
70000 401.20457 343.26271 477.7732 2448.0372 -10073.559 -7625.5221 165.48772 7.0785685e-24
|
||||
71000 402.24809 344.81761 451.63484 2454.4045 -10080.232 -7625.8277 744.0284 7.2460812e-24
|
||||
72000 399.55459 374.72185 448.9371 2437.9695 -10064.675 -7626.7056 272.84926 7.6144831e-24
|
||||
73000 395.77443 380.61122 467.77232 2414.904 -10041.316 -7626.4125 645.93262 7.3997026e-24
|
||||
74000 390.49062 347.8078 434.09228 2382.6637 -10008.374 -7625.7102 485.84117 7.4857321e-24
|
||||
75000 402.36317 344.00711 467.78251 2455.1067 -10080.557 -7625.4506 827.68657 7.6638656e-24
|
||||
76000 398.04237 343.92203 444.41844 2428.7424 -10053.548 -7624.8058 800.45171 7.6048201e-24
|
||||
77000 405.26409 348.28239 458.88491 2472.8073 -10099.592 -7626.7844 981.02843 7.3224151e-24
|
||||
78000 399.4194 321.49584 430.68752 2437.1446 -10062.896 -7625.7516 600.53295 7.3215622e-24
|
||||
79000 403.53179 376.82783 421.80565 2462.2373 -10088.271 -7626.0338 455.28811 7.6692865e-24
|
||||
80000 403.32714 366.12748 469.8043 2460.9886 -10087.918 -7626.9292 245.00002 7.6751832e-24
|
||||
81000 392.21509 348.48805 432.11278 2393.1859 -10018.865 -7625.6786 166.58597 7.5191708e-24
|
||||
82000 402.26796 367.04862 481.16174 2454.5257 -10080.408 -7625.8826 645.00409 7.2491634e-24
|
||||
83000 396.32681 333.64229 454.79231 2418.2745 -10043.624 -7625.3499 1000.8329 7.0898852e-24
|
||||
84000 396.69496 369.32897 520.98012 2420.5209 -10047.118 -7626.5967 867.6324 7.3128665e-24
|
||||
85000 400.97936 328.83063 502.79303 2446.663 -10073.092 -7626.4287 676.86462 7.3327638e-24
|
||||
86000 390.07415 322.61202 491.71376 2380.1225 -10004.873 -7624.7504 1325.0673 7.3283143e-24
|
||||
87000 401.99526 324.1684 487.46124 2452.8618 -10078.775 -7625.9136 399.22408 7.597008e-24
|
||||
88000 402.98644 401.0839 460.18142 2458.9097 -10084.956 -7626.0467 362.95913 7.4845633e-24
|
||||
89000 400.83386 352.81777 456.38861 2445.7752 -10072.352 -7626.5772 183.87748 7.1810169e-24
|
||||
90000 399.73934 337.97836 484.29339 2439.0968 -10065.83 -7626.7336 269.00825 7.2295514e-24
|
||||
91000 397.65455 317.0225 493.96737 2426.376 -10052.281 -7625.9055 252.29482 7.1717719e-24
|
||||
92000 403.29755 339.15515 487.69926 2460.808 -10086.755 -7625.9468 345.4829 7.2519632e-24
|
||||
93000 393.48816 311.01308 462.07837 2400.9538 -10026.85 -7625.8963 1087.0615 6.9548881e-24
|
||||
94000 398.27622 351.54184 490.12325 2430.1692 -10055.491 -7625.3214 47.073346 6.7970322e-24
|
||||
95000 399.0935 334.61876 435.92656 2435.1561 -10060.151 -7624.9949 299.83321 6.7981252e-24
|
||||
96000 395.53012 323.78287 432.75557 2413.4133 -10039.318 -7625.9043 -208.21009 6.596548e-24
|
||||
97000 398.3106 332.10795 453.07308 2430.379 -10056.177 -7625.798 269.3525 6.4603022e-24
|
||||
98000 393.00228 342.45211 441.02858 2397.9891 -10022.45 -7624.4611 162.65896 6.4161295e-24
|
||||
99000 402.28099 363.11445 444.60687 2454.6052 -10080.921 -7626.3159 243.55067 6.1876996e-24
|
||||
100000 393.02428 355.42659 414.49876 2398.1234 -10023.158 -7625.035 234.02585 5.8734288e-24
|
||||
101000 407.27153 356.83347 474.54541 2485.0561 -10111.82 -7626.7637 908.44737 5.9505313e-24
|
||||
102000 398.20342 347.43164 456.42536 2429.725 -10054.368 -7624.6434 923.66142 5.6405052e-24
|
||||
103000 404.57968 312.04308 491.59336 2468.6312 -10095.413 -7626.782 691.26129 5.5554657e-24
|
||||
104000 405.43656 370.15792 466.35062 2473.8597 -10100.037 -7626.1774 698.44015 5.643723e-24
|
||||
105000 397.85337 345.93414 409.72358 2427.5891 -10053.577 -7625.9874 497.6322 5.5045434e-24
|
||||
106000 387.35911 290.71163 460.62957 2363.5561 -9987.8121 -7624.2559 550.57687 5.074857e-24
|
||||
107000 400.15652 281.24457 432.10967 2441.6423 -10067.86 -7626.2173 195.26601 5.029905e-24
|
||||
108000 398.27224 368.48887 486.57848 2430.145 -10056.431 -7626.286 378.04138 4.8422966e-24
|
||||
109000 396.9247 343.69642 471.52457 2421.9226 -10047.447 -7625.5248 360.74958 4.9975924e-24
|
||||
110000 395.85201 343.42899 456.98661 2415.3774 -10040.905 -7625.5278 408.33877 5.4212292e-24
|
||||
111000 402.25599 306.55664 513.38262 2454.4527 -10080.546 -7626.0937 492.44729 5.6617717e-24
|
||||
112000 396.46861 335.49892 451.73627 2419.1397 -10045.068 -7625.9286 785.30259 5.5356068e-24
|
||||
113000 402.30232 345.23699 514.30137 2454.7354 -10080.598 -7625.8624 131.29054 5.4836368e-24
|
||||
114000 400.08702 339.87622 468.42054 2441.2183 -10067.168 -7625.95 968.41409 5.2913495e-24
|
||||
115000 398.24539 350.00505 460.96395 2429.9811 -10055.92 -7625.9389 514.62142 5.3165576e-24
|
||||
116000 405.38897 360.3222 473.93416 2473.5692 -10100.564 -7626.9943 846.62767 4.9387162e-24
|
||||
117000 384.21971 284.45465 438.53162 2344.4004 -9969.9338 -7625.5335 391.03533 4.8069594e-24
|
||||
118000 402.26326 374.64259 465.41914 2454.4971 -10079.461 -7624.9644 561.13242 5.0386599e-24
|
||||
119000 400.59392 364.77068 426.56943 2444.3112 -10070.089 -7625.7783 1050.3472 5.1388448e-24
|
||||
120000 394.94966 367.50544 464.98489 2409.8715 -10036.207 -7626.3353 435.53452 4.7605695e-24
|
||||
121000 401.0263 341.41871 483.51635 2446.9495 -10072.156 -7625.2065 -248.22261 4.6905655e-24
|
||||
122000 405.18187 365.88528 459.48636 2472.3056 -10098.464 -7626.1587 714.4055 4.8247332e-24
|
||||
123000 393.15342 349.82187 464.48254 2398.9114 -10025.675 -7626.7635 894.9725 4.4392172e-24
|
||||
124000 399.61053 314.48406 411.16635 2438.3108 -10063.983 -7625.6717 414.26792 4.4467168e-24
|
||||
125000 401.41188 360.80671 427.86684 2449.3022 -10075.024 -7625.7222 661.76562 4.5418558e-24
|
||||
126000 389.59988 322.77359 434.22566 2377.2287 -10001.795 -7624.5661 -6.6991611 4.3204896e-24
|
||||
127000 408.32753 361.06676 504.46609 2491.4995 -10118.409 -7626.9097 -46.128898 4.4314564e-24
|
||||
128000 402.6002 357.72918 513.02384 2456.553 -10083.769 -7627.2161 893.25022 4.4623147e-24
|
||||
129000 389.10117 353.91284 438.37455 2374.1857 -9999.0942 -7624.9086 321.75667 4.3154062e-24
|
||||
130000 398.00339 355.80819 460.02245 2428.5045 -10053.271 -7624.7667 301.5802 4.3048725e-24
|
||||
131000 391.77518 364.06813 452.03809 2390.5018 -10016.251 -7625.749 917.65013 4.156684e-24
|
||||
132000 399.40303 328.29985 481.9756 2437.0447 -10061.973 -7624.928 -83.253707 4.2519717e-24
|
||||
133000 391.32936 354.6152 419.72303 2387.7815 -10012.2 -7624.4185 906.78871 4.4265719e-24
|
||||
134000 393.7918 349.59071 490.77774 2402.8066 -10027.894 -7625.0874 607.98407 4.4985637e-24
|
||||
135000 396.12123 354.80195 500.60528 2417.0201 -10041.849 -7624.8289 21.769213 4.4999037e-24
|
||||
136000 407.98297 353.54435 439.70695 2489.3971 -10116.513 -7627.1161 801.90089 4.086977e-24
|
||||
137000 393.09712 361.71611 462.99109 2398.5678 -10023.663 -7625.0948 634.48425 4.0271555e-24
|
||||
138000 403.47214 358.50875 468.98438 2461.8733 -10086.575 -7624.7014 365.30875 3.7359876e-24
|
||||
139000 395.71778 314.06446 470.60903 2414.5584 -10040.681 -7626.1222 468.11183 3.5497274e-24
|
||||
140000 402.33881 336.23233 496.88193 2454.958 -10080.915 -7625.9569 558.58815 3.3647224e-24
|
||||
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289000 387.6666 329.67717 430.08944 2365.4323 -9990.077 -7624.6447 833.58067 2.5712457e-24
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293000 392.72347 329.62376 438.62819 2396.2879 -10022.429 -7626.1413 525.03485 2.1847439e-24
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294000 396.35724 342.10312 508.0937 2418.4602 -10044.218 -7625.7577 759.06278 2.0758419e-24
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296000 398.13154 309.56719 418.07669 2429.2865 -10055.194 -7625.9073 373.67063 1.9691384e-24
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297000 396.93759 349.06409 438.20318 2422.0013 -10047.747 -7625.7453 876.74739 2.083423e-24
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298000 411.82088 353.00771 510.73707 2512.8149 -10140.25 -7627.4349 451.32942 1.9806472e-24
|
||||
299000 397.08112 332.93943 446.18548 2422.8771 -10049.812 -7626.9353 1051.6015 1.9833611e-24
|
||||
300000 399.32386 305.12198 451.51497 2436.5617 -10064.061 -7627.4995 536.77963 1.9828425e-24
|
||||
301000 397.4376 365.8162 492.86209 2425.0522 -10050.868 -7625.8156 -315.5025 2.2473483e-24
|
||||
302000 403.05986 330.02057 531.10253 2459.3577 -10085.567 -7626.209 1522.0797 2.1300499e-24
|
||||
303000 404.63994 327.51587 486.57974 2468.9989 -10095.067 -7626.068 485.23122 2.2780919e-24
|
||||
304000 389.29588 312.11096 465.8965 2375.3738 -10000.368 -7624.9946 1021.3292 2.3365373e-24
|
||||
305000 389.28201 337.54357 436.71808 2375.2891 -10000.763 -7625.4737 237.17774 2.4771912e-24
|
||||
306000 397.21703 349.69205 475.90382 2423.7064 -10050.585 -7626.8782 451.49664 2.493797e-24
|
||||
307000 394.9687 325.97502 471.22207 2409.9877 -10035.267 -7625.2789 911.41151 2.6805479e-24
|
||||
308000 400.24559 346.89356 468.83991 2442.1858 -10068.645 -7626.4593 584.10123 2.8721683e-24
|
||||
309000 400.87683 333.19579 484.93965 2446.0374 -10071.793 -7625.7554 280.95614 3.017198e-24
|
||||
310000 398.70629 366.31548 430.17831 2432.7934 -10057.58 -7624.7861 194.03866 2.9388208e-24
|
||||
311000 395.29309 356.85212 454.73614 2411.967 -10038.462 -7626.4951 1513.012 2.8717806e-24
|
||||
312000 395.86192 351.98923 445.75368 2415.4379 -10041.052 -7625.6138 697.147 2.8123105e-24
|
||||
313000 398.91806 369.25296 480.25195 2434.0856 -10060.594 -7626.5088 1193.3774 3.0528649e-24
|
||||
314000 397.46908 381.74368 479.89916 2425.2443 -10051.409 -7626.1645 970.96257 2.9432432e-24
|
||||
315000 388.88575 385.65042 439.69937 2372.8713 -9998.409 -7625.5377 331.76518 2.8263791e-24
|
||||
316000 402.51549 346.1234 453.29766 2456.0361 -10082.071 -7626.0352 648.57559 2.7960817e-24
|
||||
317000 391.60087 338.87215 548.21915 2389.4381 -10014.296 -7624.8574 470.3507 2.8748585e-24
|
||||
318000 415.90486 350.77177 482.47637 2537.7342 -10164.381 -7626.6471 98.356192 3.0352123e-24
|
||||
319000 381.11161 339.62575 403.65411 2325.4357 -9950.4736 -7625.0379 812.66782 3.0714218e-24
|
||||
320000 389.61697 337.65689 500.49824 2377.3329 -10002.527 -7625.1939 402.06942 3.1984594e-24
|
||||
321000 389.22621 320.0831 462.64121 2374.9486 -10001.171 -7626.2227 702.28565 3.3334796e-24
|
||||
322000 394.87373 330.47042 434.60642 2409.4082 -10036.661 -7627.2528 996.17425 3.0170861e-24
|
||||
323000 404.11699 339.23872 481.88746 2465.808 -10092.887 -7627.0795 920.41355 2.9491648e-24
|
||||
324000 402.88315 303.23277 452.18047 2458.2795 -10085.27 -7626.991 442.97341 2.7699513e-24
|
||||
325000 392.17239 351.52226 461.91428 2392.9254 -10018.731 -7625.806 647.59343 2.7433186e-24
|
||||
326000 399.27293 348.37925 477.42217 2436.2509 -10062.656 -7626.4056 625.12988 2.9478186e-24
|
||||
327000 393.10449 325.10059 459.8579 2398.6128 -10026.09 -7627.4772 1401.8328 3.0083555e-24
|
||||
328000 400.71355 342.21843 423.13161 2445.0412 -10071.682 -7626.6404 194.36793 2.966981e-24
|
||||
329000 386.15577 340.00098 430.75104 2356.2137 -9980.7421 -7624.5284 173.23007 3.0620374e-24
|
||||
330000 391.55319 327.96031 454.03452 2389.1472 -10015.532 -7626.3845 933.42231 3.1165707e-24
|
||||
331000 395.1642 344.77984 457.7902 2411.1806 -10037.989 -7626.8089 830.00999 3.1392669e-24
|
||||
332000 398.81926 369.59815 468.47746 2433.4827 -10060.498 -7627.0153 608.22167 3.1896179e-24
|
||||
333000 400.77871 322.4412 422.66428 2445.4387 -10071.061 -7625.6218 444.52956 2.9744079e-24
|
||||
333333 394.00501 321.40483 494.893 2404.1075 -10030.441 -7626.3333 781.5773 2.92248e-24
|
||||
Loop time of 1905.78 on 32 procs for 333333 steps with 3072 atoms
|
||||
|
||||
Performance: 45.336 ns/day, 0.529 hours/ns, 174.907 timesteps/s
|
||||
100.0% CPU use with 32 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 491.27 | 637.64 | 789.54 | 375.9 | 33.46
|
||||
Bond | 0.15629 | 0.22951 | 0.30402 | 6.5 | 0.01
|
||||
Kspace | 562.21 | 704.47 | 846.18 | 336.0 | 36.97
|
||||
Neigh | 56.401 | 56.567 | 56.745 | 1.5 | 2.97
|
||||
Comm | 132.58 | 157.08 | 174.05 | 98.4 | 8.24
|
||||
Output | 0.079991 | 0.080906 | 0.088337 | 0.5 | 0.00
|
||||
Modify | 338.14 | 339.52 | 341.13 | 5.1 | 17.82
|
||||
Other | | 10.18 | | | 0.53
|
||||
|
||||
Nlocal: 96 ave 111 max 84 min
|
||||
Histogram: 2 4 0 10 3 5 2 4 1 1
|
||||
Nghost: 8407.69 ave 8550 max 8297 min
|
||||
Histogram: 2 1 9 1 8 2 5 1 2 1
|
||||
Neighs: 96320.8 ave 119221 max 72553 min
|
||||
Histogram: 2 3 4 4 3 3 4 4 2 3
|
||||
|
||||
Total # of neighbors = 3082264
|
||||
Ave neighs/atom = 1003.34
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 14579
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:31:45
|
|
@ -0,0 +1,574 @@
|
|||
|
||||
# energy flux into the reservoir
|
||||
variable F equal 0.075
|
||||
|
||||
# timestep
|
||||
variable dt equal 3.0
|
||||
|
||||
# simulation time for the production run (1 ns)
|
||||
variable tprod equal 1000000
|
||||
|
||||
# total number of timesteps
|
||||
variable Nprod equal floor(${tprod}/${dt})
|
||||
variable Nprod equal floor(1000000/${dt})
|
||||
variable Nprod equal floor(1000000/3)
|
||||
|
||||
# parameters for the SPC/E model
|
||||
variable epsOO equal 0.15535
|
||||
variable sigOO equal 3.166
|
||||
variable theta equal 109.47
|
||||
|
||||
# long-range and short-range cutoffs, respectively
|
||||
variable cutC equal (xhi-xlo)/2.
|
||||
variable cutLJ equal 11
|
||||
|
||||
# specification of units, spatial dimensions, boundary conditions and atom-style
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
read_data "data.spce"
|
||||
orthogonal box = (-12.6314 -12.6314 -25.2628) to (12.6314 12.6314 25.2628)
|
||||
2 by 4 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
3072 atoms
|
||||
reading velocities ...
|
||||
3072 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2048 bonds
|
||||
reading angles ...
|
||||
1024 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# group atoms to molecules
|
||||
group O type 2
|
||||
1024 atoms in group O
|
||||
group H type 1
|
||||
2048 atoms in group H
|
||||
group water type 1 2
|
||||
3072 atoms in group water
|
||||
|
||||
# define the pair style with long-range Coulomb interaction
|
||||
# and short-range LJ interaction
|
||||
pair_style lj/cut/coul/long ${cutLJ} ${cutC}
|
||||
pair_style lj/cut/coul/long 11 ${cutC}
|
||||
pair_style lj/cut/coul/long 11 12.6314
|
||||
pair_coeff 2 2 ${epsOO} ${sigOO}
|
||||
pair_coeff 2 2 0.15535 ${sigOO}
|
||||
pair_coeff 2 2 0.15535 3.166
|
||||
pair_coeff 1 2 0 0
|
||||
pair_coeff 1 1 0 0
|
||||
|
||||
# use Ewald summation with a precision of 1.e-5
|
||||
kspace_style ewald 1.e-5
|
||||
|
||||
# use harmonic bonds between sites of a molecules
|
||||
# NOTE: this will not have any effects as we use RATTLE to keep the bonds fixed,
|
||||
# but it is recommended.
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 ${theta}
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
# use standard correction terms for the truncated tail of the LJ potential
|
||||
pair_modify tail yes
|
||||
|
||||
# increase neigbor skin because of the large timestep
|
||||
neighbor 4.5 bin
|
||||
|
||||
variable Nsamp equal 10
|
||||
variable Nrepeat equal floor(${Nprod}/${Nsamp})
|
||||
variable Nrepeat equal floor(333333/${Nsamp})
|
||||
variable Nrepeat equal floor(333333/10)
|
||||
variable Nevery equal ${Nsamp}*${Nrepeat}
|
||||
variable Nevery equal 10*${Nrepeat}
|
||||
variable Nevery equal 10*33333
|
||||
|
||||
# compute the centre of mass velocity of the 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
|
||||
|
||||
# compute temperature, pressure, potential energy, kinetic energy and total energy
|
||||
compute cT all temp
|
||||
compute cP all pressure thermo_temp
|
||||
compute cPe all pe
|
||||
compute cKe all ke
|
||||
variable vE equal c_cKe+c_cPe
|
||||
|
||||
# specify the reservoir extents
|
||||
variable Lz equal zhi-zlo
|
||||
variable delta equal 4
|
||||
variable dz equal ${Lz}/60
|
||||
variable dz equal 50.5255/60
|
||||
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
|
||||
variable zlo_Thi equal -50.5255/4.-${delta}/2.
|
||||
variable zlo_Thi equal -50.5255/4.-4/2.
|
||||
variable zhi_Thi equal ${zlo_Thi}+${delta}
|
||||
variable zhi_Thi equal -14.631375+${delta}
|
||||
variable zhi_Thi equal -14.631375+4
|
||||
variable zlo_Tlo equal ${Lz}/4.-${delta}/2.
|
||||
variable zlo_Tlo equal 50.5255/4.-${delta}/2.
|
||||
variable zlo_Tlo equal 50.5255/4.-4/2.
|
||||
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
|
||||
variable zhi_Tlo equal 10.631375+${delta}
|
||||
variable zhi_Tlo equal 10.631375+4
|
||||
|
||||
# create regions of low and high temperature and apply thermostats
|
||||
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -14.631375 ${zhi_Thi}
|
||||
region Thi_region block INF INF INF INF -14.631375 -10.631375
|
||||
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 10.631375 ${zhi_Tlo}
|
||||
region Tlo_region block INF INF INF INF 10.631375 14.631375
|
||||
|
||||
# compute temperature of reservoirs using 3 degrees of freedom for every atom
|
||||
compute cTlo water temp/region Tlo_region
|
||||
compute cThi water temp/region Thi_region
|
||||
|
||||
# rescale temperature to correct for the constraint bonds (6 instead of 9 degrees of freedom per molecule)
|
||||
variable Tlo_act equal c_cTlo/2*3
|
||||
variable Thi_act equal c_cThi/2*3
|
||||
|
||||
# thermostat the reservoirs using the eHEX algorithm
|
||||
# NOTE: add the keyword "hex" at the end of each of the two following lines
|
||||
# if you want to use the HEX algorithm.
|
||||
|
||||
fix fHi all ehex 1 ${F} region Thi_region com constrain hex
|
||||
fix fHi all ehex 1 0.075 region Thi_region com constrain hex
|
||||
fix fLo all ehex 1 -${F} region Tlo_region com constrain hex
|
||||
fix fLo all ehex 1 -0.075 region Tlo_region com constrain hex
|
||||
|
||||
# use velocity Verlet integration
|
||||
fix fNVE all nve
|
||||
|
||||
# calculate the (kinetic) temperature from the kinetic
|
||||
# energy per atom
|
||||
# kB is Boltzmann's constant
|
||||
# NOTE: For simplicity, we do not subtract the centre of mass
|
||||
# velocity of the individual slabs in this example script.
|
||||
# However, we did take this into account in the publication.
|
||||
# (The differences are negligible for our setup.)
|
||||
|
||||
variable kB equal 0.001987204
|
||||
compute ke water ke/atom
|
||||
variable T atom c_ke/${kB}
|
||||
variable T atom c_ke/0.001987204
|
||||
|
||||
# use RATTLE with a precision of 1.e-10
|
||||
fix fRattle all rattle 1e-10 400 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1024 = # of frozen angles
|
||||
|
||||
# output the timestep, temperatures (average, cold reservoir, hot reservoir), energies (kinetic, potential and total),
|
||||
# pressure and squared com velocity every 100 timesteps
|
||||
reset_timestep 0
|
||||
timestep ${dt}
|
||||
timestep 3
|
||||
|
||||
thermo_style custom step temp v_Tlo_act v_Thi_act ke pe etotal press v_vcm2
|
||||
thermo_modify flush yes
|
||||
thermo 1000
|
||||
|
||||
compute cchT all chunk/atom bin/1d z lower ${dz}
|
||||
compute cchT all chunk/atom bin/1d z lower 0.842091666666667
|
||||
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_hex
|
||||
fix fchT all ave/chunk 10 ${Nrepeat} ${Nevery} cchT v_T file out.Tspce_hex
|
||||
fix fchT all ave/chunk 10 33333 ${Nevery} cchT v_T file out.Tspce_hex
|
||||
fix fchT all ave/chunk 10 33333 333330 cchT v_T file out.Tspce_hex
|
||||
|
||||
fix fE all ave/time 10 500 5000 v_vE file out.Espce_hex
|
||||
run ${Nprod}
|
||||
run 333333
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.234029
|
||||
estimated absolute RMS force accuracy = 0.00363217
|
||||
estimated relative force accuracy = 1.09382e-05
|
||||
KSpace vectors: actual max1d max3d = 903 11 6083
|
||||
kxmax kymax kzmax = 6 6 11
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17.1314
|
||||
ghost atom cutoff = 17.1314
|
||||
binsize = 8.5657 -> bins = 3 3 6
|
||||
Memory usage per processor = 8.42898 Mbytes
|
||||
Step Temp Tlo_act Thi_act KinEng PotEng TotEng Press vcm2
|
||||
0 399.28553 345.31026 514.38426 2436.3278 -10062.57 -7626.2426 316.77546 8.2636936e-24
|
||||
1000 408.95549 362.43567 501.1829 2495.3311 -10123.25 -7627.9188 213.21196 8.2636826e-24
|
||||
2000 407.76706 327.32795 475.04683 2488.0797 -10116.724 -7628.6441 515.85498 8.2637003e-24
|
||||
3000 404.17656 328.39288 465.74678 2466.1714 -10092.952 -7626.7805 1018.4711 8.2637905e-24
|
||||
4000 395.63918 314.76443 475.86825 2414.0787 -10040.238 -7626.1595 -314.93352 8.2637714e-24
|
||||
5000 400.45293 322.89398 466.20682 2443.4509 -10071.254 -7627.8032 540.52556 8.263785e-24
|
||||
6000 397.4985 356.00319 458.4864 2425.4238 -10054.401 -7628.9767 927.07005 8.2637319e-24
|
||||
7000 398.06805 348.57818 429.25234 2428.8991 -10056.874 -7627.9745 796.67299 8.2637356e-24
|
||||
8000 392.11696 321.54288 455.29804 2392.5872 -10019.888 -7627.3008 521.59927 8.2637327e-24
|
||||
9000 399.83694 367.58704 431.81964 2439.6923 -10068.028 -7628.3354 617.93129 8.2637e-24
|
||||
10000 389.57167 327.39661 448.50635 2377.0566 -10005.42 -7628.3639 221.25986 8.2636912e-24
|
||||
11000 401.45824 387.48254 496.15108 2449.585 -10079.26 -7629.6752 -103.92476 8.2637123e-24
|
||||
12000 405.48482 381.54583 445.59512 2474.1541 -10104.299 -7630.1448 1008.1215 8.2636789e-24
|
||||
13000 396.98637 390.67892 448.86134 2422.299 -10052.825 -7630.5263 205.61453 8.2636741e-24
|
||||
14000 397.6922 348.69762 442.17789 2426.6057 -10056.551 -7629.9453 887.3048 8.263628e-24
|
||||
15000 389.66173 354.52184 388.13667 2377.6061 -10008.305 -7630.6992 121.56817 8.2635999e-24
|
||||
16000 401.36841 356.73003 448.75459 2449.0369 -10081.197 -7632.1604 445.50568 8.2635581e-24
|
||||
17000 407.54931 350.93807 433.65799 2486.7511 -10119.92 -7633.1688 924.99137 8.2635696e-24
|
||||
18000 401.13481 326.26158 434.82289 2447.6116 -10080.02 -7632.4087 545.58495 8.263567e-24
|
||||
19000 394.38111 318.92033 517.51619 2406.4024 -10038.405 -7632.0025 3.828149 8.2635739e-24
|
||||
20000 391.30256 337.66599 449.90188 2387.618 -10019.67 -7632.0516 693.94255 8.2635881e-24
|
||||
21000 399.1952 313.28576 474.08668 2435.7766 -10068.881 -7633.104 883.23062 8.2635454e-24
|
||||
22000 410.03813 354.52597 472.93137 2501.9371 -10135.778 -7633.8406 713.38728 8.2636559e-24
|
||||
23000 401.44282 344.99613 492.71442 2449.491 -10082.955 -7633.464 959.09393 8.2636484e-24
|
||||
24000 401.36494 336.41645 416.70271 2449.0158 -10084.536 -7635.5202 379.6687 8.2636939e-24
|
||||
25000 397.3905 356.93702 417.4757 2424.7648 -10059.166 -7634.4013 9.4815402 8.2637192e-24
|
||||
26000 400.23988 343.57277 430.07257 2442.1509 -10076.962 -7634.8114 778.13747 8.2637448e-24
|
||||
27000 404.7058 402.02403 467.22557 2469.4007 -10105.928 -7636.527 1058.386 8.2637566e-24
|
||||
28000 390.25154 364.99878 495.34982 2381.2049 -10016.419 -7635.2139 1080.4999 8.2637489e-24
|
||||
29000 391.4133 360.55619 459.25074 2388.2936 -10023.522 -7635.2285 608.79953 8.2637048e-24
|
||||
30000 401.43341 359.32597 475.75694 2449.4336 -10087.103 -7637.6699 1181.7254 8.2636171e-24
|
||||
31000 410.20625 357.8459 476.87738 2502.9629 -10140.616 -7637.6535 157.40917 8.2636479e-24
|
||||
32000 398.66325 323.62162 452.85356 2432.5308 -10069.996 -7637.465 680.03303 8.2636334e-24
|
||||
33000 389.7502 345.63304 499.70088 2378.1459 -10016.009 -7637.8636 688.33171 8.2636501e-24
|
||||
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|
||||
192000 396.56672 340.17989 459.98945 2419.7383 -10114.225 -7694.4864 619.95976 8.264207e-24
|
||||
193000 402.27823 365.80197 479.73362 2454.5884 -10150.105 -7695.5167 666.78784 8.2642613e-24
|
||||
194000 393.40982 354.60412 438.34949 2400.4758 -10094.069 -7693.5929 927.75139 8.2642956e-24
|
||||
195000 405.26862 319.43491 519.67889 2472.8349 -10169.414 -7696.5789 690.73743 8.2643518e-24
|
||||
196000 396.07815 330.55295 443.56941 2416.7572 -10112.568 -7695.8108 293.28039 8.2643131e-24
|
||||
197000 380.93121 345.77783 437.92531 2324.3349 -10019.361 -7695.0258 1207.7584 8.2643599e-24
|
||||
198000 395.54525 309.49699 473.47556 2413.5056 -10111.14 -7697.6339 1640.4275 8.2643825e-24
|
||||
199000 392.84644 367.4887 430.76312 2397.0382 -10093.439 -7696.4007 511.98097 8.2643862e-24
|
||||
200000 401.96286 297.79681 480.92587 2452.6641 -10150.666 -7698.0022 707.11499 8.2643747e-24
|
||||
201000 393.00174 336.55695 447.85717 2397.9859 -10096.34 -7698.3537 553.92457 8.2643415e-24
|
||||
202000 400.96713 400.76296 427.62006 2446.5884 -10145.262 -7698.6739 1328.0071 8.2643457e-24
|
||||
203000 386.48269 317.70369 439.34682 2358.2084 -10055.445 -7697.2368 100.16455 8.264332e-24
|
||||
204000 399.8182 339.5894 442.9848 2439.578 -10140.032 -7700.4545 725.57645 8.2643026e-24
|
||||
205000 394.9499 354.19939 445.43529 2409.873 -10107.639 -7697.7659 437.61511 8.2643053e-24
|
||||
206000 398.74655 342.26259 494.51827 2433.0391 -10132.35 -7699.3107 25.261711 8.2643297e-24
|
||||
207000 397.46695 312.89505 482.89179 2425.2313 -10126.307 -7701.0761 193.74565 8.2643998e-24
|
||||
208000 396.03751 308.31104 543.26368 2416.5092 -10116.22 -7699.7107 366.31568 8.2644188e-24
|
||||
209000 393.67604 339.59434 492.72791 2402.1002 -10103.631 -7701.5309 800.72262 8.2644073e-24
|
||||
210000 397.70814 319.04632 484.3669 2426.703 -10127.775 -7701.0723 1001.1468 8.2643818e-24
|
||||
211000 394.41546 314.14769 465.17344 2406.612 -10108.978 -7702.3663 808.39403 8.2643389e-24
|
||||
212000 390.69784 316.99266 469.28829 2383.9281 -10085.964 -7702.0362 157.07183 8.2643947e-24
|
||||
213000 391.01919 349.42113 440.45432 2385.8889 -10087.53 -7701.6408 233.60596 8.2643953e-24
|
||||
214000 394.7636 377.71033 513.48127 2408.7362 -10110.491 -7701.7546 1032.684 8.2643434e-24
|
||||
215000 385.08557 351.05634 414.37425 2349.6836 -10051.745 -7702.0615 -191.73319 8.2643541e-24
|
||||
216000 395.66059 344.08093 470.02691 2414.2094 -10117.545 -7703.336 363.63998 8.2643211e-24
|
||||
217000 393.32904 353.34929 430.14078 2399.983 -10103.083 -7703.0996 826.82581 8.2642635e-24
|
||||
218000 393.26099 338.60391 480.4634 2399.5677 -10104.08 -7704.5126 1825.8367 8.2642387e-24
|
||||
219000 398.10557 346.47494 448.19001 2429.128 -10134.204 -7705.076 720.5502 8.2642673e-24
|
||||
220000 387.20841 330.85034 423.264 2362.6366 -10067.084 -7704.4472 936.68166 8.2642584e-24
|
||||
221000 395.10842 342.50828 436.855 2410.8402 -10116.548 -7705.7082 464.67433 8.2642376e-24
|
||||
222000 404.58299 333.97385 417.59997 2468.6514 -10175.441 -7706.7899 320.1926 8.2641982e-24
|
||||
223000 394.99608 301.81336 438.98488 2410.1548 -10116.432 -7706.2771 -333.07297 8.2641895e-24
|
||||
224000 399.75635 333.42156 532.69775 2439.2006 -10146.284 -7707.0838 -24.302435 8.264212e-24
|
||||
225000 387.34945 322.48978 403.67368 2363.4972 -10069.72 -7706.2232 1124.6063 8.264228e-24
|
||||
226000 392.49324 373.02591 456.69451 2394.8832 -10100.536 -7705.6528 1081.313 8.2642422e-24
|
||||
227000 389.26399 328.79668 499.39877 2375.1792 -10082.252 -7707.0731 297.23931 8.2641977e-24
|
||||
228000 395.77463 345.70356 444.92055 2414.9053 -10122.866 -7707.9612 909.88331 8.2642275e-24
|
||||
229000 399.95735 335.15167 521.27945 2440.4271 -10149.947 -7709.5198 1040.8768 8.2642067e-24
|
||||
230000 393.55741 331.44243 472.65593 2401.3764 -10110.011 -7708.6345 476.8327 8.264236e-24
|
||||
231000 390.44878 376.3162 448.01989 2382.4084 -10090.42 -7708.0111 -790.72946 8.2642989e-24
|
||||
232000 386.29548 321.29516 447.72795 2357.0661 -10065.54 -7708.4742 401.70686 8.2642975e-24
|
||||
233000 391.40903 321.50881 426.74322 2388.2676 -10097.942 -7709.6747 198.51726 8.2643182e-24
|
||||
234000 387.42985 307.20989 427.9318 2363.9878 -10073.893 -7709.9056 1009.3059 8.2643048e-24
|
||||
235000 394.49817 344.47716 471.30483 2407.1166 -10117.796 -7710.6794 116.1363 8.2643378e-24
|
||||
236000 391.22702 356.80698 453.0439 2387.157 -10097.209 -7710.0517 1171.3841 8.2642419e-24
|
||||
237000 400.47523 313.26047 508.80244 2443.587 -10154.899 -7711.3122 931.71105 8.2641944e-24
|
||||
238000 389.51089 330.64742 410.88383 2376.6857 -10087.385 -7710.6993 189.36264 8.2641658e-24
|
||||
239000 394.14901 372.01879 425.54222 2404.9861 -10117.145 -7712.1592 641.18484 8.2641561e-24
|
||||
240000 404.58466 312.3919 471.69524 2468.6616 -10181.47 -7712.8086 644.71013 8.2641576e-24
|
||||
241000 392.94544 329.39792 504.1128 2397.6424 -10109.746 -7712.1039 419.41583 8.2641563e-24
|
||||
242000 390.33516 341.83747 451.09025 2381.7151 -10093.639 -7711.9235 359.16457 8.2641766e-24
|
||||
243000 389.39599 314.61323 456.3439 2375.9846 -10088.85 -7712.8659 360.78844 8.2642306e-24
|
||||
244000 402.99921 318.93549 449.84933 2458.9876 -10173.776 -7714.7886 789.38213 8.2642756e-24
|
||||
245000 394.63556 371.70941 457.25263 2407.9549 -10123.176 -7715.2213 513.01386 8.2642274e-24
|
||||
246000 377.20119 323.97603 473.41588 2301.5753 -10014.629 -7713.0534 228.02469 8.2643014e-24
|
||||
247000 391.25299 342.69412 457.02912 2387.3155 -10102.14 -7714.8247 346.46153 8.264308e-24
|
||||
248000 388.60789 374.17857 474.19303 2371.1758 -10086.2 -7715.0247 936.72611 8.2642713e-24
|
||||
249000 386.64086 302.31198 465.4038 2359.1736 -10073.352 -7714.1787 -101.93533 8.2643988e-24
|
||||
250000 396.87797 350.03724 398.43921 2421.6375 -10138.469 -7716.8316 524.75051 8.2644281e-24
|
||||
251000 397.55209 339.67841 444.9577 2425.7508 -10144.016 -7718.2649 978.88761 8.2644734e-24
|
||||
252000 404.69406 364.54655 475.03227 2469.3291 -10186.531 -7717.202 656.1086 8.2645074e-24
|
||||
253000 387.89659 342.21563 439.10552 2366.8357 -10082.609 -7715.7734 1012.2099 8.2644436e-24
|
||||
254000 389.04273 330.24932 389.82087 2373.8291 -10091.12 -7717.2908 149.56263 8.2645143e-24
|
||||
255000 393.0951 345.81833 470.46109 2398.5555 -10116.423 -7717.8676 731.30067 8.264532e-24
|
||||
256000 387.7685 326.3846 417.74063 2366.0541 -10083.951 -7717.8966 793.77065 8.2645191e-24
|
||||
257000 400.15259 348.6024 475.57122 2441.6183 -10159.902 -7718.2833 360.76368 8.2645564e-24
|
||||
258000 386.94759 374.69297 418.71736 2361.0452 -10080.094 -7719.0489 615.68952 8.2645347e-24
|
||||
259000 395.98913 339.54171 534.48548 2416.214 -10135.749 -7719.5353 632.27398 8.2645186e-24
|
||||
260000 393.29148 328.18651 470.48418 2399.7538 -10119.207 -7719.4537 1025.1623 8.2645605e-24
|
||||
261000 395.27314 303.33824 413.94073 2411.8453 -10132.405 -7720.5593 399.25401 8.2645987e-24
|
||||
262000 392.95808 331.29971 452.68892 2397.7194 -10117.9 -7720.1801 955.51994 8.2645373e-24
|
||||
263000 391.59151 334.46468 516.16108 2389.381 -10109.919 -7720.5377 585.5697 8.2645348e-24
|
||||
264000 394.64494 357.22387 472.36074 2408.0122 -10129.21 -7721.1974 247.44449 8.2645486e-24
|
||||
265000 396.75037 310.52619 457.42687 2420.8589 -10141.773 -7720.9145 493.56204 8.2645193e-24
|
||||
266000 390.46082 370.22114 470.05406 2382.4819 -10104.206 -7721.7245 -314.02973 8.2645598e-24
|
||||
267000 391.78709 336.15512 491.86687 2390.5744 -10112.656 -7722.0812 -168.20968 8.2646057e-24
|
||||
268000 385.65473 342.85156 429.20154 2353.1565 -10074.356 -7721.1998 483.75931 8.2645689e-24
|
||||
269000 397.15976 318.06297 476.64304 2423.3569 -10146.185 -7722.828 473.67207 8.2646375e-24
|
||||
270000 381.01486 330.20372 416.09807 2324.8453 -10047.249 -7722.4038 793.39728 8.2646529e-24
|
||||
271000 404.10564 348.85971 457.99947 2465.7387 -10190.061 -7724.322 142.30379 8.2646753e-24
|
||||
272000 377.02354 320.20082 435.86659 2300.4914 -10023.514 -7723.0226 463.01714 8.2646549e-24
|
||||
273000 385.41634 306.81753 444.29261 2351.7019 -10075.956 -7724.2544 363.68599 8.2646783e-24
|
||||
274000 395.57379 364.46533 431.0481 2413.6798 -10138.248 -7724.5679 421.18242 8.2646476e-24
|
||||
275000 395.7783 384.33583 502.38681 2414.9277 -10140.381 -7725.4533 162.55936 8.2646337e-24
|
||||
276000 398.66612 348.82699 491.64824 2432.5483 -10158.406 -7725.8578 251.80969 8.2646323e-24
|
||||
277000 390.70029 349.25724 488.53004 2383.9431 -10109.593 -7725.6495 908.70992 8.264603e-24
|
||||
278000 390.81929 344.47794 454.899 2384.6691 -10111.228 -7726.5587 514.96077 8.2645508e-24
|
||||
279000 390.49239 325.2118 477.32678 2382.6745 -10109.396 -7726.7214 678.46342 8.2645811e-24
|
||||
280000 380.94651 361.68688 452.92385 2324.4282 -10050.347 -7725.9185 672.92368 8.2645641e-24
|
||||
281000 397.38588 322.21068 461.12234 2424.7367 -10154.036 -7729.2994 603.99135 8.264554e-24
|
||||
282000 394.67148 307.63506 494.86154 2408.1742 -10135.854 -7727.6802 147.4694 8.2645608e-24
|
||||
283000 390.69597 320.29828 491.82101 2383.9167 -10111.89 -7727.9734 368.51645 8.2645941e-24
|
||||
284000 392.66955 325.04772 481.01062 2395.9589 -10123.557 -7727.5984 486.11384 8.2645316e-24
|
||||
285000 391.09771 351.87523 480.36105 2386.368 -10114.167 -7727.7994 199.01873 8.2645767e-24
|
||||
286000 395.42126 324.07456 523.04039 2412.7491 -10141.437 -7728.688 635.6432 8.2646419e-24
|
||||
287000 399.40681 325.60709 482.08917 2437.0678 -10167.438 -7730.3705 539.34881 8.2646809e-24
|
||||
288000 395.75838 378.02761 452.1086 2414.8061 -10146.131 -7731.3253 -209.99565 8.2647025e-24
|
||||
289000 403.84944 311.19207 431.66743 2464.1755 -10194.425 -7730.2498 -455.55697 8.2646732e-24
|
||||
290000 386.9779 334.74047 426.4262 2361.2301 -10090.371 -7729.1411 1027.1239 8.2646707e-24
|
||||
291000 396.80533 345.00239 431.92304 2421.1943 -10152.521 -7731.3263 476.7639 8.2646037e-24
|
||||
292000 390.09518 303.47358 474.04207 2380.2508 -10111.828 -7731.5774 660.75324 8.2645253e-24
|
||||
293000 386.26064 339.98319 427.82968 2356.8535 -10087.975 -7731.1217 538.99616 8.2644474e-24
|
||||
294000 394.82945 346.64012 444.3336 2409.138 -10141.741 -7732.6031 478.19664 8.2644788e-24
|
||||
295000 396.45415 317.19738 464.73093 2419.0515 -10151.364 -7732.3123 1029.6266 8.2644492e-24
|
||||
296000 391.73943 324.23547 476.7067 2390.2836 -10121.906 -7731.6222 1468.7909 8.2644807e-24
|
||||
297000 396.43673 349.52095 427.45136 2418.9452 -10152.01 -7733.0653 389.60884 8.2645608e-24
|
||||
298000 396.09547 343.80973 443.2879 2416.8629 -10149.843 -7732.9799 -332.27663 8.2645661e-24
|
||||
299000 405.55442 367.87033 449.3781 2474.5788 -10209.026 -7734.4472 -123.2398 8.2645583e-24
|
||||
300000 394.63029 309.97997 469.50595 2407.9228 -10141.805 -7733.8817 757.03411 8.2645733e-24
|
||||
301000 393.71578 349.24463 490.48253 2402.3428 -10136.086 -7733.7432 476.8234 8.2645812e-24
|
||||
302000 384.07144 342.10955 431.09535 2343.4957 -10077.615 -7734.1194 557.60759 8.2645448e-24
|
||||
303000 389.77061 304.16714 489.09315 2378.2704 -10112.25 -7733.9797 515.21552 8.2645334e-24
|
||||
304000 377.05163 326.48277 452.03931 2300.6628 -10034.316 -7733.6534 707.61199 8.2645482e-24
|
||||
305000 380.08253 333.16569 441.20747 2319.1565 -10054.151 -7734.9948 498.57621 8.2645811e-24
|
||||
306000 403.40825 366.43922 479.23566 2461.4835 -10197.598 -7736.1146 -70.562613 8.2646162e-24
|
||||
307000 391.4093 327.63056 443.37712 2388.2692 -10124.423 -7736.1535 501.79005 8.2645942e-24
|
||||
308000 387.49936 355.06856 539.02026 2364.4119 -10100.67 -7736.2578 894.14562 8.264578e-24
|
||||
309000 400.22623 370.21436 455.2524 2442.0676 -10179.41 -7737.3425 23.228591 8.2645348e-24
|
||||
310000 393.47325 373.38423 433.88319 2400.8629 -10138.1 -7737.2372 351.65893 8.2645142e-24
|
||||
311000 392.37405 339.33063 408.0325 2394.1559 -10131.694 -7737.538 961.25355 8.264554e-24
|
||||
312000 385.90975 329.02683 461.16365 2354.7125 -10090.947 -7736.2342 589.16035 8.2645679e-24
|
||||
313000 395.24192 349.35628 474.55861 2411.6548 -10150.814 -7739.1592 205.42197 8.2645342e-24
|
||||
314000 385.27186 342.75249 435.65557 2350.8203 -10088.721 -7737.9003 332.91246 8.2645559e-24
|
||||
315000 395.47642 337.67281 430.71992 2413.0857 -10152.228 -7739.1422 531.44453 8.2645701e-24
|
||||
316000 389.26105 333.46025 449.39932 2375.1612 -10114.153 -7738.9921 -47.00791 8.2645052e-24
|
||||
317000 391.4451 349.7595 435.2089 2388.4877 -10127.803 -7739.3155 1180.9782 8.2644829e-24
|
||||
318000 391.09544 307.36964 441.56618 2386.3541 -10125.476 -7739.122 104.73629 8.2644945e-24
|
||||
319000 390.9058 317.87654 440.72129 2385.197 -10126.801 -7741.6036 361.34383 8.2644429e-24
|
||||
320000 384.79724 320.26734 491.85426 2347.9243 -10088.296 -7740.3722 443.56585 8.2644308e-24
|
||||
321000 391.36239 327.13545 446.2889 2387.983 -10129.23 -7741.2466 595.50022 8.2644085e-24
|
||||
322000 388.31021 327.03244 436.38551 2369.3595 -10110.776 -7741.4166 354.24786 8.2644381e-24
|
||||
323000 389.51774 322.90841 516.66529 2376.7275 -10117.848 -7741.1203 668.08437 8.264442e-24
|
||||
324000 385.7225 327.82488 467.80806 2353.57 -10095.65 -7742.0805 54.848914 8.2643455e-24
|
||||
325000 379.5928 336.90832 386.27249 2316.1683 -10057.439 -7741.2702 48.389722 8.2643708e-24
|
||||
326000 386.69257 347.16202 453.93952 2359.4891 -10102.014 -7742.5254 433.68555 8.2644532e-24
|
||||
327000 393.22547 361.28156 432.71447 2399.351 -10142.847 -7743.4961 1055.6935 8.2644952e-24
|
||||
328000 389.20379 350.69102 415.12594 2374.8118 -10117.855 -7743.0431 1358.5483 8.2645242e-24
|
||||
329000 391.52016 344.35617 430.68101 2388.9456 -10131.913 -7742.9672 1061.7888 8.2645204e-24
|
||||
330000 380.0051 317.25415 422.53892 2318.684 -10062.066 -7743.382 794.49364 8.2644049e-24
|
||||
331000 387.38737 324.04786 390.41016 2363.7286 -10107.725 -7743.9965 1348.1281 8.2644758e-24
|
||||
332000 391.77155 349.33971 466.67126 2390.4796 -10135.431 -7744.9516 248.40722 8.2644493e-24
|
||||
333000 385.52137 343.14164 416.95616 2352.3427 -10097.324 -7744.9809 -257.52237 8.2645218e-24
|
||||
333333 392.07117 337.35735 449.63887 2392.3078 -10139.176 -7746.8685 204.81545 8.2645448e-24
|
||||
Loop time of 1891.87 on 32 procs for 333333 steps with 3072 atoms
|
||||
|
||||
Performance: 45.669 ns/day, 0.526 hours/ns, 176.193 timesteps/s
|
||||
100.0% CPU use with 32 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 490.28 | 639.94 | 790.46 | 380.4 | 33.83
|
||||
Bond | 0.168 | 0.22874 | 0.34386 | 8.5 | 0.01
|
||||
Kspace | 562.73 | 705.09 | 841.14 | 343.8 | 37.27
|
||||
Neigh | 56.376 | 56.511 | 56.595 | 0.9 | 2.99
|
||||
Comm | 135.4 | 152.15 | 172.14 | 94.3 | 8.04
|
||||
Output | 0.0782 | 0.079079 | 0.087162 | 0.5 | 0.00
|
||||
Modify | 327.37 | 328.26 | 329.41 | 3.4 | 17.35
|
||||
Other | | 9.6 | | | 0.51
|
||||
|
||||
Nlocal: 96 ave 116 max 81 min
|
||||
Histogram: 4 0 5 3 9 3 4 3 0 1
|
||||
Nghost: 8408.75 ave 8497 max 8297 min
|
||||
Histogram: 2 1 1 3 6 7 2 3 3 4
|
||||
Neighs: 96402.1 ave 126185 max 66771 min
|
||||
Histogram: 1 0 8 2 7 4 1 5 2 2
|
||||
|
||||
Total # of neighbors = 3084867
|
||||
Ave neighs/atom = 1004.19
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 14509
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:31:31
|
|
@ -0,0 +1,73 @@
|
|||
# Time-averaged data for fix fE
|
||||
# TimeStep v_E
|
||||
10000 -8215.16
|
||||
20000 -8215.15
|
||||
30000 -8215.16
|
||||
40000 -8215.16
|
||||
50000 -8215.15
|
||||
60000 -8215.17
|
||||
70000 -8215.16
|
||||
80000 -8215.17
|
||||
90000 -8215.16
|
||||
100000 -8215.16
|
||||
110000 -8215.17
|
||||
120000 -8215.16
|
||||
130000 -8215.17
|
||||
140000 -8215.17
|
||||
150000 -8215.18
|
||||
160000 -8215.17
|
||||
170000 -8215.17
|
||||
180000 -8215.18
|
||||
190000 -8215.17
|
||||
200000 -8215.18
|
||||
210000 -8215.17
|
||||
220000 -8215.18
|
||||
230000 -8215.17
|
||||
240000 -8215.18
|
||||
250000 -8215.17
|
||||
260000 -8215.19
|
||||
270000 -8215.18
|
||||
280000 -8215.18
|
||||
290000 -8215.18
|
||||
300000 -8215.19
|
||||
310000 -8215.18
|
||||
320000 -8215.18
|
||||
330000 -8215.19
|
||||
340000 -8215.19
|
||||
350000 -8215.2
|
||||
360000 -8215.19
|
||||
370000 -8215.19
|
||||
380000 -8215.18
|
||||
390000 -8215.19
|
||||
400000 -8215.19
|
||||
410000 -8215.19
|
||||
420000 -8215.19
|
||||
430000 -8215.17
|
||||
440000 -8215.19
|
||||
450000 -8215.2
|
||||
460000 -8215.2
|
||||
470000 -8215.19
|
||||
480000 -8215.18
|
||||
490000 -8215.18
|
||||
500000 -8215.19
|
||||
510000 -8215.18
|
||||
520000 -8215.18
|
||||
530000 -8215.17
|
||||
540000 -8215.18
|
||||
550000 -8215.18
|
||||
560000 -8215.19
|
||||
570000 -8215.17
|
||||
580000 -8215.18
|
||||
590000 -8215.17
|
||||
600000 -8215.18
|
||||
610000 -8215.18
|
||||
620000 -8215.17
|
||||
630000 -8215.17
|
||||
640000 -8215.18
|
||||
650000 -8215.17
|
||||
660000 -8215.19
|
||||
670000 -8215.17
|
||||
680000 -8215.17
|
||||
690000 -8215.17
|
||||
700000 -8215.18
|
||||
710000 -8215.17
|
|
@ -0,0 +1,73 @@
|
|||
# Time-averaged data for fix fE
|
||||
# TimeStep v_E
|
||||
10000 -8215.46
|
||||
20000 -8216.01
|
||||
30000 -8216.57
|
||||
40000 -8217.11
|
||||
50000 -8217.61
|
||||
60000 -8218.12
|
||||
70000 -8218.62
|
||||
80000 -8219.11
|
||||
90000 -8219.61
|
||||
100000 -8220.14
|
||||
110000 -8220.65
|
||||
120000 -8221.12
|
||||
130000 -8221.64
|
||||
140000 -8222.17
|
||||
150000 -8222.68
|
||||
160000 -8223.22
|
||||
170000 -8223.68
|
||||
180000 -8224.18
|
||||
190000 -8224.72
|
||||
200000 -8225.22
|
||||
210000 -8225.76
|
||||
220000 -8226.27
|
||||
230000 -8226.77
|
||||
240000 -8227.23
|
||||
250000 -8227.74
|
||||
260000 -8228.28
|
||||
270000 -8228.8
|
||||
280000 -8229.35
|
||||
290000 -8229.85
|
||||
300000 -8230.37
|
||||
310000 -8230.89
|
||||
320000 -8231.39
|
||||
330000 -8231.89
|
||||
340000 -8232.41
|
||||
350000 -8232.92
|
||||
360000 -8233.52
|
||||
370000 -8234.05
|
||||
380000 -8234.58
|
||||
390000 -8235.14
|
||||
400000 -8235.69
|
||||
410000 -8236.21
|
||||
420000 -8236.78
|
||||
430000 -8237.34
|
||||
440000 -8237.88
|
||||
450000 -8238.41
|
||||
460000 -8238.85
|
||||
470000 -8239.4
|
||||
480000 -8239.95
|
||||
490000 -8240.46
|
||||
500000 -8241.01
|
||||
510000 -8241.53
|
||||
520000 -8242.07
|
||||
530000 -8242.63
|
||||
540000 -8243.21
|
||||
550000 -8243.7
|
||||
560000 -8244.23
|
||||
570000 -8244.8
|
||||
580000 -8245.27
|
||||
590000 -8245.8
|
||||
600000 -8246.34
|
||||
610000 -8246.92
|
||||
620000 -8247.45
|
||||
630000 -8247.95
|
||||
640000 -8248.45
|
||||
650000 -8248.98
|
||||
660000 -8249.5
|
||||
670000 -8250.04
|
||||
680000 -8250.56
|
||||
690000 -8251.08
|
||||
700000 -8251.64
|
||||
710000 -8252.2
|
|
@ -0,0 +1,68 @@
|
|||
# Time-averaged data for fix fE
|
||||
# TimeStep v_vE
|
||||
5000 -7625.81
|
||||
10000 -7625.78
|
||||
15000 -7625.85
|
||||
20000 -7625.75
|
||||
25000 -7625.75
|
||||
30000 -7625.72
|
||||
35000 -7625.71
|
||||
40000 -7625.75
|
||||
45000 -7625.8
|
||||
50000 -7625.69
|
||||
55000 -7625.85
|
||||
60000 -7625.89
|
||||
65000 -7625.9
|
||||
70000 -7625.84
|
||||
75000 -7625.83
|
||||
80000 -7625.85
|
||||
85000 -7625.79
|
||||
90000 -7625.75
|
||||
95000 -7625.66
|
||||
100000 -7625.77
|
||||
105000 -7625.77
|
||||
110000 -7625.67
|
||||
115000 -7625.73
|
||||
120000 -7625.79
|
||||
125000 -7625.9
|
||||
130000 -7625.77
|
||||
135000 -7625.78
|
||||
140000 -7625.74
|
||||
145000 -7625.76
|
||||
150000 -7625.79
|
||||
155000 -7625.92
|
||||
160000 -7625.83
|
||||
165000 -7625.97
|
||||
170000 -7625.95
|
||||
175000 -7625.93
|
||||
180000 -7626.09
|
||||
185000 -7626
|
||||
190000 -7625.99
|
||||
195000 -7626
|
||||
200000 -7625.97
|
||||
205000 -7625.84
|
||||
210000 -7625.85
|
||||
215000 -7625.96
|
||||
220000 -7625.98
|
||||
225000 -7625.91
|
||||
230000 -7625.82
|
||||
235000 -7625.94
|
||||
240000 -7625.85
|
||||
245000 -7625.96
|
||||
250000 -7626.02
|
||||
255000 -7626.07
|
||||
260000 -7626.15
|
||||
265000 -7626.07
|
||||
270000 -7626.11
|
||||
275000 -7626.13
|
||||
280000 -7626.13
|
||||
285000 -7626.13
|
||||
290000 -7626.03
|
||||
295000 -7626.12
|
||||
300000 -7626.14
|
||||
305000 -7626.04
|
||||
310000 -7626.03
|
||||
315000 -7625.98
|
||||
320000 -7626.05
|
||||
325000 -7626.07
|
||||
330000 -7626.11
|
|
@ -0,0 +1,68 @@
|
|||
# Time-averaged data for fix fE
|
||||
# TimeStep v_vE
|
||||
5000 -7626.81
|
||||
10000 -7628.63
|
||||
15000 -7630.19
|
||||
20000 -7631.84
|
||||
25000 -7633.74
|
||||
30000 -7635.52
|
||||
35000 -7637.35
|
||||
40000 -7638.97
|
||||
45000 -7640.71
|
||||
50000 -7642.63
|
||||
55000 -7644.32
|
||||
60000 -7646.14
|
||||
65000 -7647.76
|
||||
70000 -7649.48
|
||||
75000 -7651.26
|
||||
80000 -7653.14
|
||||
85000 -7654.83
|
||||
90000 -7656.73
|
||||
95000 -7658.58
|
||||
100000 -7660.28
|
||||
105000 -7662.11
|
||||
110000 -7664.01
|
||||
115000 -7666.13
|
||||
120000 -7668.06
|
||||
125000 -7669.82
|
||||
130000 -7671.8
|
||||
135000 -7673.61
|
||||
140000 -7675.55
|
||||
145000 -7677.31
|
||||
150000 -7679.02
|
||||
155000 -7680.73
|
||||
160000 -7682.28
|
||||
165000 -7683.95
|
||||
170000 -7685.72
|
||||
175000 -7687.73
|
||||
180000 -7689.52
|
||||
185000 -7691.34
|
||||
190000 -7692.88
|
||||
195000 -7694.5
|
||||
200000 -7696.31
|
||||
205000 -7698.01
|
||||
210000 -7699.86
|
||||
215000 -7701.93
|
||||
220000 -7703.76
|
||||
225000 -7705.56
|
||||
230000 -7707.55
|
||||
235000 -7709.41
|
||||
240000 -7711.29
|
||||
245000 -7712.99
|
||||
250000 -7714.89
|
||||
255000 -7716.87
|
||||
260000 -7718.7
|
||||
265000 -7720.66
|
||||
270000 -7722.43
|
||||
275000 -7724.31
|
||||
280000 -7726.03
|
||||
285000 -7727.87
|
||||
290000 -7729.7
|
||||
295000 -7731.29
|
||||
300000 -7732.93
|
||||
305000 -7734.66
|
||||
310000 -7736.41
|
||||
315000 -7738.12
|
||||
320000 -7739.79
|
||||
325000 -7741.75
|
||||
330000 -7743.66
|
|
@ -0,0 +1,64 @@
|
|||
# Chunk-averaged data for fix fchT and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_T
|
||||
714280 60 2000
|
||||
1 -10.4037 33.2882 0.725353
|
||||
2 -10.051 33.1938 0.730819
|
||||
3 -9.69833 33.1172 0.740017
|
||||
4 -9.34567 32.9538 0.746894
|
||||
5 -8.993 32.8862 0.754229
|
||||
6 -8.64033 32.7892 0.762471
|
||||
7 -8.28767 32.6527 0.771202
|
||||
8 -7.935 32.4129 0.780034
|
||||
9 -7.58233 32.5465 0.787824
|
||||
10 -7.22967 32.1852 0.795519
|
||||
11 -6.877 32.168 0.806027
|
||||
12 -6.52433 32.132 0.814674
|
||||
13 -6.17167 31.8215 0.829561
|
||||
14 -5.819 31.8406 0.836694
|
||||
15 -5.46633 31.8237 0.840473
|
||||
16 -5.11367 31.7517 0.841688
|
||||
17 -4.761 31.8169 0.837255
|
||||
18 -4.40833 31.9601 0.828371
|
||||
19 -4.05567 32.0554 0.814949
|
||||
20 -3.703 32.1904 0.805309
|
||||
21 -3.35033 32.3302 0.795665
|
||||
22 -2.99767 32.3517 0.788281
|
||||
23 -2.645 32.571 0.779732
|
||||
24 -2.29233 32.6989 0.772619
|
||||
25 -1.93967 32.7326 0.764307
|
||||
26 -1.587 32.8903 0.756355
|
||||
27 -1.23433 32.9503 0.748218
|
||||
28 -0.881667 33.1168 0.741328
|
||||
29 -0.529 33.1957 0.732696
|
||||
30 -0.176333 33.3382 0.723901
|
||||
31 0.176333 33.3665 0.717226
|
||||
32 0.529 33.5674 0.708957
|
||||
33 0.881667 33.5851 0.702687
|
||||
34 1.23433 33.7128 0.695348
|
||||
35 1.587 33.8104 0.687174
|
||||
36 1.93967 33.9639 0.680716
|
||||
37 2.29233 34.0115 0.672422
|
||||
38 2.645 34.1252 0.665054
|
||||
39 2.99767 34.3133 0.658834
|
||||
40 3.35033 34.3158 0.649396
|
||||
41 3.703 34.4385 0.642267
|
||||
42 4.05567 34.5813 0.635612
|
||||
43 4.40833 34.6516 0.621132
|
||||
44 4.761 34.7362 0.615598
|
||||
45 5.11367 34.8099 0.612928
|
||||
46 5.46633 34.6841 0.611491
|
||||
47 5.819 34.8337 0.615543
|
||||
48 6.17167 34.7095 0.620463
|
||||
49 6.52433 34.4237 0.635328
|
||||
50 6.877 34.5977 0.641225
|
||||
51 7.22967 34.2998 0.649247
|
||||
52 7.58233 34.2826 0.656613
|
||||
53 7.935 34.2375 0.664305
|
||||
54 8.28767 33.9696 0.671334
|
||||
55 8.64033 33.996 0.678592
|
||||
56 8.993 33.8433 0.68749
|
||||
57 9.34567 33.7378 0.695141
|
||||
58 9.69833 33.6676 0.702504
|
||||
59 10.051 33.4919 0.709855
|
||||
60 10.4037 33.474 0.716928
|
|
@ -0,0 +1,64 @@
|
|||
# Chunk-averaged data for fix fchT and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_T
|
||||
714280 60 2000
|
||||
1 -10.4037 33.2651 0.720524
|
||||
2 -10.051 33.2326 0.728168
|
||||
3 -9.69833 33.1321 0.736032
|
||||
4 -9.34567 32.9605 0.745455
|
||||
5 -8.993 32.8571 0.752
|
||||
6 -8.64033 32.8126 0.759782
|
||||
7 -8.28767 32.5862 0.767108
|
||||
8 -7.935 32.5255 0.776452
|
||||
9 -7.58233 32.4923 0.783464
|
||||
10 -7.22967 32.2233 0.793245
|
||||
11 -6.877 32.1649 0.802152
|
||||
12 -6.52433 32.0597 0.809727
|
||||
13 -6.17167 31.894 0.825893
|
||||
14 -5.819 31.8201 0.834171
|
||||
15 -5.46633 31.7923 0.836544
|
||||
16 -5.11367 31.7582 0.83769
|
||||
17 -4.761 31.847 0.834145
|
||||
18 -4.40833 31.8665 0.826387
|
||||
19 -4.05567 32.0177 0.811472
|
||||
20 -3.703 32.2362 0.802039
|
||||
21 -3.35033 32.1863 0.794662
|
||||
22 -2.99767 32.4707 0.784306
|
||||
23 -2.645 32.5029 0.777432
|
||||
24 -2.29233 32.5492 0.769146
|
||||
25 -1.93967 32.8207 0.760055
|
||||
26 -1.587 32.8207 0.752244
|
||||
27 -1.23433 32.9672 0.744905
|
||||
28 -0.881667 33.0893 0.736732
|
||||
29 -0.529 33.1797 0.728727
|
||||
30 -0.176333 33.3123 0.722114
|
||||
31 0.176333 33.3939 0.714863
|
||||
32 0.529 33.529 0.706935
|
||||
33 0.881667 33.6331 0.697971
|
||||
34 1.23433 33.7068 0.691524
|
||||
35 1.587 33.9242 0.683565
|
||||
36 1.93967 33.8761 0.677874
|
||||
37 2.29233 34.0981 0.668683
|
||||
38 2.645 34.1325 0.66107
|
||||
39 2.99767 34.2494 0.653961
|
||||
40 3.35033 34.4148 0.646727
|
||||
41 3.703 34.4164 0.638381
|
||||
42 4.05567 34.5422 0.631481
|
||||
43 4.40833 34.7204 0.61733
|
||||
44 4.761 34.7482 0.610725
|
||||
45 5.11367 34.804 0.607364
|
||||
46 5.46633 34.8341 0.607692
|
||||
47 5.819 34.7501 0.610449
|
||||
48 6.17167 34.7132 0.616666
|
||||
49 6.52433 34.5599 0.630396
|
||||
50 6.877 34.5142 0.638963
|
||||
51 7.22967 34.2706 0.645295
|
||||
52 7.58233 34.3693 0.653337
|
||||
53 7.935 34.0976 0.660834
|
||||
54 8.28767 34.0633 0.669231
|
||||
55 8.64033 34.0347 0.677084
|
||||
56 8.993 33.6612 0.684168
|
||||
57 9.34567 33.9232 0.691087
|
||||
58 9.69833 33.5585 0.698545
|
||||
59 10.051 33.5071 0.70595
|
||||
60 10.4037 33.5109 0.712599
|
|
@ -0,0 +1,64 @@
|
|||
# Chunk-averaged data for fix fchT and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_T
|
||||
333330 60 3072
|
||||
1 -24.8417 51.1789 399.587
|
||||
2 -23.9996 51.3344 404.04
|
||||
3 -23.1575 50.9332 407.958
|
||||
4 -22.3154 50.6123 413.354
|
||||
5 -21.4733 50.1793 415.842
|
||||
6 -20.6312 50.0233 420.672
|
||||
7 -19.7892 50.1993 424.701
|
||||
8 -18.9471 49.9245 429.644
|
||||
9 -18.105 49.6798 432.804
|
||||
10 -17.2629 49.2232 437.029
|
||||
11 -16.4208 48.9359 442.501
|
||||
12 -15.5787 48.867 447.344
|
||||
13 -14.7366 48.6395 452.899
|
||||
14 -13.8945 48.0897 459.966
|
||||
15 -13.0524 48.2255 462.581
|
||||
16 -12.2103 48.2437 462.161
|
||||
17 -11.3682 48.2114 459.743
|
||||
18 -10.5261 48.4836 453.907
|
||||
19 -9.68405 48.8839 447.493
|
||||
20 -8.84196 48.9365 443.272
|
||||
21 -7.99987 49.2293 439.17
|
||||
22 -7.15778 49.676 434.747
|
||||
23 -6.31569 49.9824 429.981
|
||||
24 -5.4736 49.8396 426.136
|
||||
25 -4.6315 50.2061 421.495
|
||||
26 -3.78941 50.3845 417.377
|
||||
27 -2.94732 50.5774 413.029
|
||||
28 -2.10523 50.7688 409.147
|
||||
29 -1.26314 51.1003 405.638
|
||||
30 -0.421046 50.9692 400.513
|
||||
31 0.421046 51.3682 396.892
|
||||
32 1.26314 51.7177 393.407
|
||||
33 2.10523 51.884 388.909
|
||||
34 2.94732 51.9704 384.617
|
||||
35 3.78941 52.3543 380.911
|
||||
36 4.6315 52.4771 377.217
|
||||
37 5.4736 52.2991 372.769
|
||||
38 6.31569 52.7152 369.066
|
||||
39 7.15778 52.8089 364.107
|
||||
40 7.99987 52.9698 360.36
|
||||
41 8.84196 53.1409 356.529
|
||||
42 9.68405 53.3444 351.577
|
||||
43 10.5261 53.4758 346.309
|
||||
44 11.3682 53.9071 340.567
|
||||
45 12.2103 53.9105 339.045
|
||||
46 13.0524 54.024 339.392
|
||||
47 13.8945 53.987 341.271
|
||||
48 14.7366 53.5267 346.761
|
||||
49 15.5787 53.4169 351.082
|
||||
50 16.4208 53.1345 356.502
|
||||
51 17.2629 52.8734 359.928
|
||||
52 18.105 52.9656 363.932
|
||||
53 18.9471 52.6152 368.133
|
||||
54 19.7892 52.3686 372.142
|
||||
55 20.6312 52.2453 375.257
|
||||
56 21.4733 52.1108 379.516
|
||||
57 22.3154 52.0382 383.843
|
||||
58 23.1575 51.7649 387.614
|
||||
59 23.9996 51.702 391.539
|
||||
60 24.8417 51.3453 395.098
|
|
@ -0,0 +1,64 @@
|
|||
# Chunk-averaged data for fix fchT and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_T
|
||||
333330 60 3072
|
||||
1 -24.8417 51.2597 397.471
|
||||
2 -23.9996 51.114 400.974
|
||||
3 -23.1575 50.8477 405.71
|
||||
4 -22.3154 50.605 410.569
|
||||
5 -21.4733 50.5218 414.883
|
||||
6 -20.6312 50.1361 420.139
|
||||
7 -19.7892 49.9089 422.847
|
||||
8 -18.9471 49.9605 427.665
|
||||
9 -18.105 49.6702 431.239
|
||||
10 -17.2629 49.1298 436.204
|
||||
11 -16.4208 48.8757 441.209
|
||||
12 -15.5787 48.6389 445.325
|
||||
13 -14.7366 48.4831 451.589
|
||||
14 -13.8945 48.0754 457.211
|
||||
15 -13.0524 48.1373 459.481
|
||||
16 -12.2103 48.0212 460.14
|
||||
17 -11.3682 47.9667 457.168
|
||||
18 -10.5261 48.5215 449.876
|
||||
19 -9.68405 48.9601 444.096
|
||||
20 -8.84196 49.0186 439.7
|
||||
21 -7.99987 49.2077 435.575
|
||||
22 -7.15778 49.62 431.368
|
||||
23 -6.31569 49.5686 426.605
|
||||
24 -5.4736 49.9916 421.589
|
||||
25 -4.6315 50.4944 417.502
|
||||
26 -3.78941 50.4292 413.508
|
||||
27 -2.94732 50.659 408.675
|
||||
28 -2.10523 51.1448 404.226
|
||||
29 -1.26314 51.2025 400.408
|
||||
30 -0.421046 51.1445 395.959
|
||||
31 0.421046 51.514 392.289
|
||||
32 1.26314 51.7346 388.088
|
||||
33 2.10523 51.6179 383.72
|
||||
34 2.94732 52.0298 379.939
|
||||
35 3.78941 52.2917 376.025
|
||||
36 4.6315 52.0233 372.255
|
||||
37 5.4736 52.6806 368.337
|
||||
38 6.31569 52.7248 364.799
|
||||
39 7.15778 52.6929 359.932
|
||||
40 7.99987 53.0972 356.253
|
||||
41 8.84196 53.2178 351.894
|
||||
42 9.68405 53.2878 347.989
|
||||
43 10.5261 53.3249 342.746
|
||||
44 11.3682 53.9685 337.277
|
||||
45 12.2103 54.0029 335.83
|
||||
46 13.0524 53.8822 335.208
|
||||
47 13.8945 53.6381 337.254
|
||||
48 14.7366 53.7767 342.471
|
||||
49 15.5787 53.4807 346.974
|
||||
50 16.4208 53.0637 352.003
|
||||
51 17.2629 53.08 355.799
|
||||
52 18.105 52.7805 360.048
|
||||
53 18.9471 52.7732 363.682
|
||||
54 19.7892 52.5654 368.224
|
||||
55 20.6312 52.1811 371.756
|
||||
56 21.4733 52.092 376.621
|
||||
57 22.3154 52.2272 380.327
|
||||
58 23.1575 51.8835 385.252
|
||||
59 23.9996 51.6008 388.17
|
||||
60 24.8417 51.4517 393.014
|
|
@ -152,6 +152,10 @@ The ELASTIC_T directory has an example script for computing elastic
|
|||
constants at finite temperature, using an Si example. See the
|
||||
ELASTIC_T/in.elastic file for more info.
|
||||
|
||||
The HEAT directory has example scripts for heat exchange algorithms
|
||||
(e.g. used for establishing a thermal gradient), using two different
|
||||
methods. See the HEAT/README file for more info.
|
||||
|
||||
The KAPPA directory has example scripts for computing the thermal
|
||||
conductivity (kappa) of a LJ liquid using 4 different methods. See
|
||||
the KAPPA/README file for more info.
|
||||
|
|
Loading…
Reference in New Issue