jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15020 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-05-10 22:39:37 +00:00
parent 5253f2aae1
commit 1463cb2598
19 changed files with 16049 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4018
examples/HEAT/data.lj Normal file
View File

File diff suppressed because it is too large Load Diff

9245
examples/HEAT/data.spce Normal file
View File

File diff suppressed because it is too large Load Diff

132
examples/HEAT/in.lj_ehex Normal file
View File

@ -0,0 +1,132 @@
###############################################################################
#
#
# This input script is a modified version of the example script lj_ehex.lmp
# which is part of the supplementary (open access) material of the paper
#
# P. Wirnsberger, D. Frenkel and C. Dellago,
# "An enhanced version of the heat exchange algorithm with excellent energy
# conservation properties", J. Chem. Phys. 143, 124104 (2015).
#
# The full article is available on arXiv: http://arxiv.org/pdf/1507.07081.
#
#
# Description:
# ------------
#
# This file is a LAMMPS input script for carrying out a NEMD simulation of
# Lennard-Jones using the eHEX/a algorithm. The run produces two files:
# "out.Tlj_ehex" contains the temperature profile and "out.Elj_ehex" the time
# evolution of the total energy.
#
###############################################################################
log log.lj_ehex
# heat flux
variable J equal 0.15
# timestep
variable dt equal 0.007
# cutoff radius for shifted LJ-potential
variable rc equal 3.0
# simulation time for the production run
variable tprod equal 5000
# total number of timesteps
variable Nprod equal floor(${tprod}/${dt})
# equilibrated steady state configuration
read_data "data.lj"
# use LJ shifted force pair style
pair_style lj/sf ${rc}
# with coefficients eps = 1, sigma = 1, and rc = 3.0
pair_coeff 1 1 1.0 1.0 ${rc}
# increase neigbor skin because of the large timestep
neighbor 0.8 bin
# options used for fix ave/time; sample the quantities every 10 steps
variable Nsamp equal 10
variable Nrepeat equal floor(${Nprod}/${Nsamp})
variable Nevery equal ${Nsamp}*${Nrepeat}
# box dimensions
variable Lz equal zhi-zlo
variable Lx equal xhi-xlo
variable Ly equal yhi-ylo
# reservoir width in z-direction
variable delta equal 2.
# specify z-extents of both reservoirs
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
variable zhi_Thi equal ${zlo_Thi}+${delta}
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
# resolution for fix ave/spatial
variable dz equal ${Lz}/60
# compute per-atom kinetic energy and temperature, respectively
# NOTE: In this example we ignored the centre of mass (com) velocities
# of the individual bins for simplicity. However, we took that
# into account for the publication.
compute ke all ke/atom
variable T atom c_ke/1.5
# specify the reservoirs
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
# compute the temperature of the individual region
compute cTlo all temp/region Tlo_region
compute cThi all temp/region Thi_region
# calculate the energy flux from the specified heat flux
variable F equal ${J}*${Lx}*${Ly}*2.
# use fix ehex to create the gradient
# hot reservoir
fix fHi all ehex 1 +${F} region Thi_region
# cold reservoir
fix fLo all ehex 1 -${F} 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}
# frequency for console output
thermo 10000
# print timestep, temperature, total energy and v_com^2 to console
thermo_style custom step temp etotal v_vcm2
# calculate spatial average of temperature
compute cchT all chunk/atom bin/1d z lower ${dz}
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_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
# production run
run ${Nprod}

132
examples/HEAT/in.lj_hex Normal file
View File

@ -0,0 +1,132 @@
###############################################################################
#
#
# This input script is a modified version of the example script lj_hex.lmp
# which is part of the supplementary (open access) material of the paper
#
# P. Wirnsberger, D. Frenkel and C. Dellago,
# "An enhanced version of the heat exchange algorithm with excellent energy
# conservation properties", J. Chem. Phys. 143, 124104 (2015).
#
# The full article is available on arXiv: http://arxiv.org/pdf/1507.07081.
#
#
# Description:
# ------------
#
# This file is a LAMMPS input script for carrying out a NEMD simulation of
# Lennard-Jones using the HEX/a algorithm. The run produces two files:
# "out.Tlj_hex" contains the temperature profile and "out.Elj_hex" the time
# evolution of the total energy.
#
###############################################################################
log log.lj_hex
# heat flux
variable J equal 0.15
# timestep
variable dt equal 0.007
# cutoff radius for shifted LJ-potential
variable rc equal 3.0
# simulation time for the production run
variable tprod equal 5000
# total number of timesteps
variable Nprod equal floor(${tprod}/${dt})
# equilibrated steady state configuration
read_data "data.lj"
# use LJ shifted force pair style
pair_style lj/sf ${rc}
# with coefficients eps = 1, sigma = 1, and rc = 3.0
pair_coeff 1 1 1.0 1.0 ${rc}
# increase neigbor skin because of the large timestep
neighbor 0.8 bin
# options used for fix ave/time; sample the quantities every 10 steps
variable Nsamp equal 10
variable Nrepeat equal floor(${Nprod}/${Nsamp})
variable Nevery equal ${Nsamp}*${Nrepeat}
# box dimensions
variable Lz equal zhi-zlo
variable Lx equal xhi-xlo
variable Ly equal yhi-ylo
# reservoir width in z-direction
variable delta equal 2.
# specify z-extents of both reservoirs
variable zlo_Thi equal -${Lz}/4.-${delta}/2.
variable zhi_Thi equal ${zlo_Thi}+${delta}
variable zlo_Tlo equal ${zlo_Thi}+${Lz}/2.
variable zhi_Tlo equal ${zlo_Tlo}+${delta}
# resolution for fix ave/spatial
variable dz equal ${Lz}/60
# compute per-atom kinetic energy and temperature, respectively
# NOTE: In this example we ignored the centre of mass (com) velocities
# of the individual bins for simplicity. However, we took that
# into account for the publication.
compute ke all ke/atom
variable T atom c_ke/1.5
# specify the reservoirs
region Thi_region block INF INF INF INF ${zlo_Thi} ${zhi_Thi}
region Tlo_region block INF INF INF INF ${zlo_Tlo} ${zhi_Tlo}
# compute the temperature of the individual region
compute cTlo all temp/region Tlo_region
compute cThi all temp/region Thi_region
# calculate the energy flux from the specified heat flux
variable F equal ${J}*${Lx}*${Ly}*2.
# use fix ehex to create the gradient
# hot reservoir
fix fHi all ehex 1 +${F} region Thi_region hex
# cold reservoir
fix fLo all ehex 1 -${F} region Tlo_region hex
# use velocity Verlet for integration
fix fNVEGrad all nve
# calculate the centre of mass velocity of the entire box (vcmx, vcmy, vcmz)
variable vcmx equal "vcm(all,x)"
variable vcmy equal "vcm(all,y)"
variable vcmz equal "vcm(all,z)"
variable vcm2 equal v_vcmx*v_vcmx+v_vcmy*v_vcmy+v_vcmz*v_vcmz
# specify the timestep
timestep ${dt}
# frequency for console output
thermo 10000
# print timestep, temperature, total energy and v_com^2 to console
thermo_style custom step temp etotal v_vcm2
# calculate spatial average of temperature
compute cchT all chunk/atom bin/1d z lower ${dz}
fix fchT all ave/chunk ${Nsamp} ${Nrepeat} ${Nevery} cchT v_T file out.Tlj_hex
# compute the total energy
compute cKe all ke
compute cPe all pe
variable E equal c_cKe+c_cPe
# track the time evolution of the total energy
fix fE all ave/time ${Nsamp} 1000 10000 v_E file out.Elj_hex
# production run
run ${Nprod}

160
examples/HEAT/in.spce_ehex Normal file
View File

@ -0,0 +1,160 @@
###############################################################################
#
#
# This input script is a modified version of the example script spce_ehex.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 eHEX/a algorithm. The run produces two files:
# "out.Tspce_ehex" contains the temperature profile and "out.Espce_ehex" the time
# evolution of the total energy.
#
###############################################################################
log log.spce_ehex
# 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 ${theta}
# increase neigbor skin because of the large timestep
neighbor 4.5 bin
# use standard correction terms for the truncated tail of the LJ potential
pair_modify tail yes
variable Nsamp equal 10
variable Nrepeat equal floor(${Nprod}/${Nsamp})
variable 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 ${F} region Thi_region com constrain
fix fLo all ehex 1 -${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}

160
examples/HEAT/in.spce_hex Normal file
View File

@ -0,0 +1,160 @@
###############################################################################
#
#
# 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}

256
examples/HEAT/log.lj_ehex Normal file
View File

@ -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

256
examples/HEAT/log.lj_hex Normal file
View File

@ -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

574
examples/HEAT/log.spce_ehex Normal file
View File

@ -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
141000 390.27311 311.07374 460.05198 2381.3365 -10007.429 -7626.093 1126.8545 3.2464282e-24
142000 393.63824 339.93599 419.39374 2401.8696 -10027.564 -7625.6945 741.0209 3.0500788e-24
143000 397.51164 331.0469 450.07627 2425.504 -10050.831 -7625.3266 668.38301 2.9083564e-24
144000 393.10328 337.6981 472.92882 2398.6054 -10023.507 -7624.9016 493.81006 2.9618102e-24
145000 406.38479 394.90718 483.2248 2479.6455 -10105.256 -7625.6103 999.81877 3.0006594e-24
146000 386.23682 360.04959 479.11361 2356.7082 -9982.775 -7626.0668 338.90869 3.0263624e-24
147000 399.57593 418.81942 512.6819 2438.0997 -10065.085 -7626.985 1194.2439 2.9955393e-24
148000 397.35439 315.44391 472.69151 2424.5445 -10050.52 -7625.9754 451.53093 3.0100605e-24
149000 394.12491 380.02425 408.51492 2404.8392 -10031.083 -7626.2439 253.6796 3.0589257e-24
150000 403.59725 352.43453 499.30639 2462.6367 -10089.322 -7626.6854 521.76119 2.9051286e-24
151000 411.04746 349.0499 484.08982 2508.0958 -10135.255 -7627.1592 600.27043 2.5982318e-24
152000 403.51604 319.64743 428.71981 2462.1411 -10088.937 -7626.7959 26.849024 2.3946638e-24
153000 403.40176 340.48804 441.59862 2461.4438 -10088.61 -7627.1665 827.88922 2.316269e-24
154000 405.53367 355.70091 436.25612 2474.4521 -10099.674 -7625.222 490.99264 2.4678031e-24
155000 400.78843 341.64124 436.47144 2445.4981 -10071.909 -7626.4105 607.27858 2.3797742e-24
156000 396.11532 350.70785 424.30209 2416.9841 -10043.775 -7626.7907 318.74073 2.3998673e-24
157000 389.67493 344.0027 403.60101 2377.6866 -10002.293 -7624.6059 952.70176 2.3265128e-24
158000 396.23545 344.1557 429.0811 2417.717 -10043.065 -7625.3478 1037.6685 2.3626373e-24
159000 407.99217 370.96606 497.23585 2489.4533 -10115.3 -7625.8468 896.0355 2.3867422e-24
160000 393.62903 363.20338 483.53257 2401.8134 -10028.029 -7626.2153 18.982122 2.3178532e-24
161000 402.19382 350.07102 502.13815 2454.0733 -10079.194 -7625.1206 1344.1046 2.3487567e-24
162000 409.73384 397.93184 474.84486 2500.0804 -10126.965 -7626.8843 557.48305 2.4443243e-24
163000 403.90942 363.92703 478.61439 2464.5414 -10090.372 -7625.8307 874.92821 2.3901083e-24
164000 388.29684 332.92305 452.89948 2369.2779 -9994.1853 -7624.9074 546.89103 2.3413479e-24
165000 402.41433 341.28128 435.15747 2455.4188 -10081.494 -7626.0751 787.35918 2.4437769e-24
166000 403.15317 368.12735 440.48244 2459.927 -10086.946 -7627.0193 -0.082343245 2.6386448e-24
167000 396.12653 341.87452 509.32043 2417.0525 -10042.974 -7625.9213 -63.465634 2.6836346e-24
168000 397.98611 362.06119 470.06293 2428.3991 -10054.512 -7626.113 -65.65398 2.6397055e-24
169000 395.65107 331.3532 457.3665 2414.1513 -10040.94 -7626.7888 953.30921 2.6508809e-24
170000 405.17785 361.89133 519.29864 2472.281 -10099.674 -7627.3929 978.60531 2.6657749e-24
171000 391.98619 296.8539 440.84861 2391.7893 -10016.513 -7624.7239 896.83305 2.8029635e-24
172000 408.46287 355.74097 476.00118 2492.3253 -10119.661 -7627.3354 693.91542 2.8307766e-24
173000 397.99234 332.84806 454.28894 2428.4371 -10054.684 -7626.247 -175.00825 2.7574006e-24
174000 392.10841 300.51673 430.60655 2392.535 -10018.229 -7625.6945 414.07751 2.8465499e-24
175000 394.51808 329.62736 432.70896 2407.2381 -10032.84 -7625.6018 810.08892 2.8236298e-24
176000 401.68143 332.82942 487.45548 2450.9469 -10076.064 -7625.1167 713.15409 2.7657072e-24
177000 388.50372 363.97148 443.5911 2370.5402 -9996.3921 -7625.8519 1090.2469 2.5786322e-24
178000 406.72966 335.25219 511.44457 2481.7497 -10108.747 -7626.9968 60.481514 2.5352686e-24
179000 395.72328 325.87235 440.98487 2414.5919 -10040.263 -7625.6709 668.51595 2.5353211e-24
180000 394.073 338.20129 447.35452 2404.5224 -10030.064 -7625.5415 653.25957 2.5395636e-24
181000 396.96603 346.73572 457.02916 2422.1748 -10048.808 -7626.633 1110.3032 2.6464078e-24
182000 402.03734 371.03394 429.36217 2453.1185 -10078.935 -7625.8161 530.14085 2.6911507e-24
183000 393.03494 374.72208 436.60435 2398.1884 -10023.841 -7625.6529 648.57531 2.821661e-24
184000 398.81133 364.87729 415.16621 2433.4343 -10060.4 -7626.9654 435.847 3.0215296e-24
185000 398.94886 328.67528 489.20508 2434.2735 -10060.327 -7626.054 866.50927 3.2623882e-24
186000 389.25434 320.99829 437.30886 2375.1203 -9999.7248 -7624.6046 440.73504 3.1369706e-24
187000 398.9748 340.63365 461.25132 2434.4318 -10059.303 -7624.8714 839.54498 3.1663682e-24
188000 399.93842 343.28871 466.33292 2440.3115 -10067.465 -7627.153 468.72611 3.1787629e-24
189000 403.09938 343.74503 440.08245 2459.5988 -10086.808 -7627.2091 566.58979 3.4072406e-24
190000 395.34905 337.18717 507.65774 2412.3085 -10038.545 -7626.2361 -209.64188 3.3640705e-24
191000 396.31129 335.89382 503.59303 2418.1798 -10044.73 -7626.5503 719.81309 3.4770364e-24
192000 400.61476 327.35146 436.98699 2444.4383 -10071.015 -7626.5767 271.00571 3.6612726e-24
193000 397.8767 347.4753 442.34784 2427.7315 -10054.526 -7626.7949 445.44674 3.69672e-24
194000 395.88763 361.87678 516.54857 2415.5947 -10041.115 -7625.5204 194.16998 3.8955637e-24
195000 396.77874 325.47465 484.66617 2421.032 -10045.895 -7624.8632 433.64912 3.906499e-24
196000 392.11857 305.90206 488.53702 2392.597 -10019.034 -7626.4372 402.83347 3.9310963e-24
197000 397.61243 367.90282 439.94067 2426.119 -10051.997 -7625.878 456.17269 3.842385e-24
198000 399.33669 306.52537 492.09899 2436.6399 -10063.728 -7627.0879 915.17397 4.0060258e-24
199000 400.51955 363.80724 481.72393 2443.8574 -10068.708 -7624.8503 1047.5056 3.9033275e-24
200000 399.73898 344.49817 431.59457 2439.0946 -10064.326 -7625.2318 598.07345 3.7676544e-24
201000 406.24948 391.8137 442.60097 2478.8199 -10103.941 -7625.1212 1421.96 3.6110403e-24
202000 400.87777 333.53185 458.80233 2446.0432 -10072.335 -7626.292 1510.5447 3.5002246e-24
203000 401.36899 340.54087 475.97374 2449.0404 -10075.428 -7626.3875 1182.0064 3.57839e-24
204000 400.35802 333.42887 511.21419 2442.8718 -10069.589 -7626.7169 857.91447 3.6446527e-24
205000 398.16682 314.86187 503.01898 2429.5017 -10055.999 -7626.4974 -121.37967 3.5859517e-24
206000 396.68636 310.0794 527.56571 2420.4684 -10045.814 -7625.3453 660.02951 3.4754187e-24
207000 401.61616 358.191 470.47674 2450.5486 -10077.386 -7626.8377 674.82334 3.5732951e-24
208000 393.75424 301.36564 487.30651 2402.5774 -10028.328 -7625.751 1185.8885 3.8878621e-24
209000 403.35999 371.18162 461.57686 2461.189 -10087.401 -7626.2119 452.2842 4.0203787e-24
210000 398.44251 343.1152 453.37361 2431.1839 -10057.378 -7626.1938 841.54655 4.1618995e-24
211000 398.25764 349.60409 452.59431 2430.0559 -10056.18 -7626.1246 947.69445 3.9271884e-24
212000 401.84369 337.02027 450.23587 2451.9369 -10078.83 -7626.893 1439.1528 4.0329445e-24
213000 391.92045 347.77459 426.29934 2391.3881 -10017.847 -7626.4586 525.49553 4.1234371e-24
214000 400.74086 377.19948 449.37998 2445.2078 -10071.418 -7626.2098 -155.19145 4.1605987e-24
215000 398.31295 361.11591 463.33853 2430.3934 -10056.81 -7626.4163 296.54132 4.1636916e-24
216000 397.74679 370.39978 455.88449 2426.9388 -10052.719 -7625.7799 1059.5209 4.0720695e-24
217000 390.75587 327.95719 434.16548 2384.2822 -10009.733 -7625.4509 324.95337 4.1682488e-24
218000 402.72477 348.71632 457.14832 2457.3131 -10082.911 -7625.5981 69.602677 4.1090414e-24
219000 388.93567 366.48637 444.01487 2373.1758 -9997.9798 -7624.804 755.00377 4.0500302e-24
220000 399.50813 366.15563 419.50883 2437.686 -10063.664 -7625.9781 159.21585 4.1219917e-24
221000 396.83731 338.16861 452.91809 2421.3895 -10047.196 -7625.8068 598.16232 4.0158066e-24
222000 403.71671 370.97397 474.39211 2463.3656 -10089.809 -7626.4437 548.83762 3.9121806e-24
223000 399.86077 369.93748 466.61067 2439.8377 -10066.223 -7626.3856 694.022 3.9116486e-24
224000 399.07429 335.21246 505.95139 2435.0389 -10061.194 -7626.1552 828.72273 3.609313e-24
225000 393.28433 317.07644 444.84567 2399.7101 -10024.995 -7625.2852 145.4723 3.7230943e-24
226000 392.75218 330.81959 491.43357 2396.4631 -10022.073 -7625.6099 198.51211 3.6492732e-24
227000 396.16385 327.42798 436.57804 2417.2802 -10042.535 -7625.2544 -73.444501 3.673556e-24
228000 389.85571 338.98951 497.5617 2378.7897 -10004.777 -7625.9874 781.91292 3.6630275e-24
229000 399.47369 348.17878 512.80573 2437.4759 -10064.015 -7626.5389 540.19425 3.4966895e-24
230000 392.99734 337.6426 485.01956 2397.959 -10023.18 -7625.2209 245.54594 3.4917031e-24
231000 402.1704 326.71146 448.87017 2453.9304 -10080.734 -7626.8039 626.11619 3.3965511e-24
232000 399.77126 363.72298 467.28106 2439.2916 -10066.678 -7627.3863 111.7073 3.4047098e-24
233000 402.08669 349.37976 408.386 2453.4197 -10079.358 -7625.9381 416.28687 3.4298021e-24
234000 406.64506 299.277 458.04576 2481.2336 -10108.748 -7627.5148 167.2598 3.4449528e-24
235000 394.32368 343.17935 497.58442 2406.052 -10030.811 -7624.759 432.47872 3.4090739e-24
236000 394.43629 381.45732 477.27495 2406.7391 -10032.573 -7625.8338 929.00777 3.2836525e-24
237000 399.30893 372.53483 446.76493 2436.4705 -10062.765 -7626.2949 778.58092 3.2995246e-24
238000 399.03681 341.10557 464.05726 2434.8102 -10061.826 -7627.0158 610.89156 3.3395727e-24
239000 396.38251 319.50241 479.25532 2418.6143 -10043.64 -7625.0257 843.21988 3.4195989e-24
240000 396.13572 385.6302 440.12991 2417.1085 -10042.743 -7625.6345 413.16513 3.3351272e-24
241000 406.91046 368.78466 483.73359 2482.8529 -10108.536 -7625.683 493.55359 3.4604847e-24
242000 389.27692 343.53759 459.17945 2375.258 -9999.529 -7624.271 609.13643 3.4641767e-24
243000 389.27932 305.05682 464.66059 2375.2727 -10000.941 -7625.6682 1175.3163 3.5224437e-24
244000 406.66435 319.6153 470.00726 2481.3513 -10109.113 -7627.7618 387.43252 3.4380413e-24
245000 393.88892 349.98199 438.68239 2403.3992 -10029.086 -7625.687 684.73678 3.3999299e-24
246000 403.65952 347.82612 436.11425 2463.0166 -10089.479 -7626.4626 106.97003 3.2760664e-24
247000 404.39785 341.26879 488.05061 2467.5217 -10094.643 -7627.1213 513.01765 3.1883993e-24
248000 396.78873 335.60415 466.87975 2421.093 -10046.669 -7625.5758 920.31631 3.255637e-24
249000 393.11472 341.56045 475.52691 2398.6753 -10024.894 -7626.2192 196.44641 3.2136539e-24
250000 402.6381 384.80764 464.19682 2456.7842 -10084.363 -7627.5786 858.7842 3.1731854e-24
251000 394.44538 335.82213 441.05031 2406.7946 -10032.381 -7625.586 618.01063 3.1916498e-24
252000 392.39633 311.13226 470.22042 2394.2918 -10019.233 -7624.9407 402.35013 3.3386173e-24
253000 400.12702 317.34326 488.94448 2441.4623 -10068.275 -7626.8128 1119.6593 3.0579933e-24
254000 406.7875 354.3461 460.82698 2482.1027 -10109.228 -7627.1257 313.39098 3.1350702e-24
255000 405.86519 318.31803 472.07681 2476.475 -10103.069 -7626.5938 562.36432 3.121776e-24
256000 409.89045 362.66522 464.0064 2501.036 -10128.721 -7627.6852 957.52986 2.8327401e-24
257000 405.78579 353.68052 428.875 2475.9905 -10102.282 -7626.2919 727.40285 2.8738479e-24
258000 403.68242 363.9549 520.29528 2463.1563 -10088.536 -7625.3802 -490.68173 2.7886387e-24
259000 387.57853 329.40073 447.86134 2364.8949 -9991.0551 -7626.1602 521.95078 2.8386917e-24
260000 391.05812 365.87938 478.06218 2386.1264 -10011.877 -7625.7511 457.51312 2.609663e-24
261000 396.61688 352.29609 474.19165 2420.0444 -10045.644 -7625.5997 1012.6263 2.6002298e-24
262000 393.33469 340.8646 461.32023 2400.0174 -10026.963 -7626.9456 -113.20972 2.5131648e-24
263000 394.0413 330.96611 486.17652 2404.329 -10029.415 -7625.0865 375.64681 2.3775021e-24
264000 392.93318 337.84884 418.7966 2397.5675 -10023.643 -7626.0758 615.92641 2.3720438e-24
265000 397.50427 329.48614 429.35169 2425.459 -10051.103 -7625.6436 687.95084 2.3103281e-24
266000 401.13847 347.97779 441.33349 2447.6339 -10074.496 -7626.8625 899.78472 2.2811998e-24
267000 392.54052 373.1295 461.94227 2395.1716 -10021.891 -7626.7192 1303.2652 2.2007216e-24
268000 405.90121 353.33495 496.48525 2476.6948 -10102.756 -7626.0608 475.64632 2.2508669e-24
269000 394.70706 344.54853 494.77008 2408.3913 -10034.182 -7625.7909 833.28155 2.2166793e-24
270000 402.75785 331.48439 462.59586 2457.5149 -10084.33 -7626.8149 548.47704 2.3827304e-24
271000 405.39602 339.19548 443.01669 2473.6122 -10100.42 -7626.8077 435.51484 2.515116e-24
272000 386.52846 315.38559 483.06637 2358.4877 -9983.7484 -7625.2607 1097.0257 2.4624015e-24
273000 396.91674 351.36419 445.8735 2421.8741 -10048.514 -7626.6401 595.5938 2.5568556e-24
274000 394.53055 299.56357 424.52621 2407.3142 -10032.543 -7625.2289 550.58264 2.5236127e-24
275000 403.69265 334.39146 460.94774 2463.2188 -10090.446 -7627.2273 614.697 2.6470858e-24
276000 393.47257 336.40897 444.12831 2400.8587 -10026.396 -7625.5371 611.99703 2.7943925e-24
277000 396.58451 350.9375 464.29726 2419.8469 -10046.314 -7626.467 214.98907 2.9341478e-24
278000 403.54315 352.75172 483.72167 2462.3066 -10089.194 -7626.8877 299.11711 2.8858595e-24
279000 402.41107 359.41469 415.05668 2455.3989 -10083.498 -7628.0994 204.57354 2.7926453e-24
280000 397.44628 340.421 476.27591 2425.1052 -10050.689 -7625.5834 405.18825 2.8410989e-24
281000 402.10749 321.86806 484.33232 2453.5466 -10080.481 -7626.9344 603.56053 2.7858167e-24
282000 392.15826 342.86691 445.62376 2392.8392 -10018.753 -7625.9142 115.81024 2.6474981e-24
283000 384.4924 307.41049 436.5028 2346.0643 -9970.8975 -7624.8332 520.18192 2.7383591e-24
284000 400.11036 334.90303 432.70324 2441.3606 -10068.036 -7626.6757 264.43649 2.7884823e-24
285000 396.11833 367.05352 424.2972 2417.0024 -10043.542 -7626.5395 26.20131 2.8720199e-24
286000 396.26339 349.40869 434.25759 2417.8875 -10044.091 -7626.2033 329.98235 2.9244957e-24
287000 400.10361 362.90567 423.88278 2441.3195 -10067.784 -7626.4648 607.81647 2.7256047e-24
288000 391.9022 346.28096 471.69693 2391.2768 -10016.23 -7624.9529 820.96213 2.6576805e-24
289000 387.6666 329.67717 430.08944 2365.4323 -9990.077 -7624.6447 833.58067 2.5712457e-24
290000 393.6273 334.60262 420.57452 2401.8028 -10027.981 -7626.1783 476.85459 2.5994833e-24
291000 409.29641 312.70395 445.78229 2497.4114 -10123.797 -7626.3852 406.62784 2.4889697e-24
292000 401.86561 348.16904 462.0247 2452.0707 -10076.438 -7624.3672 586.25435 2.3508111e-24
293000 392.72347 329.62376 438.62819 2396.2879 -10022.429 -7626.1413 525.03485 2.1847439e-24
294000 396.35724 342.10312 508.0937 2418.4602 -10044.218 -7625.7577 759.06278 2.0758419e-24
295000 399.36699 376.49234 449.97982 2436.8248 -10062.943 -7626.1187 426.30173 2.1804118e-24
296000 398.13154 309.56719 418.07669 2429.2865 -10055.194 -7625.9073 373.67063 1.9691384e-24
297000 396.93759 349.06409 438.20318 2422.0013 -10047.747 -7625.7453 876.74739 2.083423e-24
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

574
examples/HEAT/log.spce_hex Normal file
View File

@ -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
34000 393.93633 341.14525 419.90896 2403.6885 -10041.074 -7637.385 366.42613 8.2637109e-24
35000 388.94933 338.42961 482.68949 2373.2592 -10012.136 -7638.8772 142.885 8.2638248e-24
36000 388.02702 345.04214 447.2788 2367.6315 -10006.3 -7638.6681 838.89823 8.263869e-24
37000 398.15249 351.05556 456.39805 2429.4143 -10068.412 -7638.9974 150.14282 8.2637612e-24
38000 402.83115 308.0906 452.25668 2457.9621 -10096.465 -7638.5026 709.74726 8.2637503e-24
39000 403.00784 333.14445 469.30889 2459.0403 -10097.76 -7638.7196 1321.8073 8.263693e-24
40000 402.28703 325.16284 475.81211 2454.6421 -10094.57 -7639.9275 501.08199 8.2636915e-24
41000 390.52404 291.83219 510.00424 2382.8676 -10023.072 -7640.2045 934.12018 8.2636618e-24
42000 389.0047 364.54323 455.44916 2373.597 -10013.789 -7640.1916 510.00764 8.2636582e-24
43000 404.04876 361.47688 467.57018 2465.3917 -10106.416 -7641.0244 901.35398 8.2636626e-24
44000 395.02967 348.03324 454.835 2410.3597 -10051.15 -7640.7901 596.01916 8.2637136e-24
45000 399.64041 307.01208 458.80168 2438.4932 -10079.598 -7641.1052 327.8297 8.2637381e-24
46000 395.38095 341.26584 493.4372 2412.5031 -10054.737 -7642.2343 349.5963 8.2637966e-24
47000 390.02957 345.72337 428.33013 2379.8505 -10021.609 -7641.7582 1733.5232 8.2637663e-24
48000 405.27371 357.46809 426.94549 2472.866 -10115.762 -7642.8964 587.69385 8.2637927e-24
49000 390.96844 359.02822 444.45547 2385.5792 -10027.241 -7641.6613 529.34881 8.2638203e-24
50000 398.02026 323.2325 474.09348 2428.6075 -10072.249 -7643.6417 859.17743 8.2638052e-24
51000 409.47764 334.83525 459.6816 2498.5171 -10143.037 -7644.5197 882.87259 8.2637846e-24
52000 397.97844 299.62548 453.42619 2428.3523 -10071.921 -7643.5686 615.38909 8.2637405e-24
53000 403.29291 353.10266 469.67277 2460.7796 -10106.463 -7645.683 1438.6929 8.2636974e-24
54000 403.64814 323.45099 466.86747 2462.9472 -10108.24 -7645.293 695.79243 8.2636476e-24
55000 390.53066 327.78611 443.31311 2382.908 -10027.345 -7644.4367 208.51316 8.2636746e-24
56000 394.48798 319.42651 433.73058 2407.0545 -10052.833 -7645.7788 816.79561 8.2636745e-24
57000 395.79064 369.56503 466.27911 2415.0029 -10060.544 -7645.5406 706.89374 8.2636544e-24
58000 400.84677 378.56404 478.60546 2445.854 -10091.523 -7645.6693 315.62704 8.263686e-24
59000 395.41467 343.93214 421.24045 2412.7089 -10059.816 -7647.1072 839.21878 8.2636771e-24
60000 397.41234 345.16324 502.45313 2424.8981 -10072.482 -7647.5841 498.68229 8.2636958e-24
61000 387.88081 294.26428 433.60646 2366.7394 -10013.264 -7646.5243 65.803393 8.2636783e-24
62000 400.3606 358.33091 434.22631 2442.8876 -10089.918 -7647.0308 214.02783 8.2636568e-24
63000 399.90474 349.52556 443.04081 2440.106 -10088.52 -7648.4145 427.79655 8.2635932e-24
64000 402.3636 321.48649 466.43244 2455.1093 -10103.607 -7648.4976 386.97717 8.2636017e-24
65000 388.4304 326.5171 443.30174 2370.0929 -10018.467 -7648.3743 127.04554 8.2636425e-24
66000 410.24127 331.72631 493.82163 2503.1766 -10152.646 -7649.4697 517.54865 8.2637075e-24
67000 396.9793 302.20693 559.22218 2422.2558 -10071.905 -7649.6488 209.28221 8.2637574e-24
68000 397.34042 381.72785 457.29533 2424.4593 -10073.949 -7649.4899 807.40949 8.2637293e-24
69000 391.36594 338.53088 444.88257 2388.0047 -10038.469 -7650.4646 547.66867 8.2637245e-24
70000 394.73445 378.46164 460.59938 2408.5583 -10058.455 -7649.8969 221.74279 8.2637143e-24
71000 398.65869 330.20631 446.4648 2432.503 -10083.219 -7650.7158 251.02858 8.2636921e-24
72000 400.84418 359.38912 496.83716 2445.8382 -10097.327 -7651.4891 392.14417 8.263673e-24
73000 396.07349 376.45322 431.91689 2416.7288 -10067.651 -7650.9218 1214.9382 8.2636748e-24
74000 404.77827 327.12692 451.59795 2469.843 -10122.675 -7652.832 701.81547 8.2637129e-24
75000 399.23023 322.07838 499.31558 2435.9904 -10088.126 -7652.1356 593.48316 8.2637515e-24
76000 395.24143 357.27737 410.08832 2411.6518 -10064.192 -7652.5403 1104.5215 8.2637136e-24
77000 396.67907 365.63782 438.94261 2420.4239 -10073.265 -7652.8416 726.07947 8.263682e-24
78000 393.96128 373.2248 430.76311 2403.8407 -10058.195 -7654.3543 515.10236 8.2636858e-24
79000 393.30172 343.99468 486.36495 2399.8163 -10052.511 -7652.6948 892.15891 8.2637334e-24
80000 393.55203 362.46411 424.30426 2401.3436 -10056.049 -7654.7058 714.32756 8.2637672e-24
81000 403.16031 363.34871 426.45664 2459.9706 -10114.788 -7654.8176 213.84624 8.2636596e-24
82000 389.65866 317.73614 416.11421 2377.5873 -10032.291 -7654.7035 262.56608 8.2636798e-24
83000 393.21909 330.65606 437.35057 2399.3121 -10053.146 -7653.8343 210.09469 8.2636918e-24
84000 398.27532 335.60609 471.48618 2430.1638 -10085.74 -7655.5758 834.46592 8.2637447e-24
85000 387.82124 302.77644 488.41406 2366.3759 -10020.661 -7654.2854 807.71014 8.263719e-24
86000 393.47457 335.11044 438.92233 2400.8709 -10056.842 -7655.9711 484.75416 8.263745e-24
87000 403.00582 328.26363 452.36381 2459.028 -10115.23 -7656.2016 758.13619 8.2636842e-24
88000 406.61793 380.16834 463.52086 2481.068 -10139.846 -7658.7778 698.97536 8.2636404e-24
89000 399.61083 354.93779 498.33374 2438.3127 -10096.456 -7658.1436 695.39104 8.2636345e-24
90000 393.17303 362.73734 470.83671 2399.031 -10057.285 -7658.2541 361.45581 8.2636763e-24
91000 399.45117 368.49392 496.94881 2437.3385 -10095.429 -7658.0906 668.32122 8.2635846e-24
92000 399.04433 352.10655 454.30239 2434.856 -10092.954 -7658.0982 289.82822 8.2635253e-24
93000 395.35025 345.52216 472.1327 2412.3158 -10069.85 -7657.5347 347.19697 8.2635497e-24
94000 404.68141 363.43683 470.23593 2469.2519 -10129.523 -7660.2709 581.20908 8.2635791e-24
95000 396.93787 380.17308 507.70163 2422.003 -10081.388 -7659.3851 865.76441 8.263647e-24
96000 403.49851 327.44245 438.9928 2462.0342 -10122.29 -7660.2558 715.42019 8.2635615e-24
97000 394.48997 336.39483 432.25803 2407.0666 -10067.139 -7660.0723 525.86352 8.2636098e-24
98000 381.70843 348.40989 448.02978 2329.0773 -9988.9847 -7659.9074 957.4232 8.2635917e-24
99000 395.60577 324.03314 524.41801 2413.8749 -10074.554 -7660.6788 -78.713018 8.2635994e-24
100000 391.4379 329.04642 459.47213 2388.4438 -10049.065 -7660.621 284.94062 8.2635869e-24
101000 400.84861 351.2835 445.97482 2445.8653 -10106.966 -7661.1011 602.28405 8.263514e-24
102000 391.57154 303.61809 458.52383 2389.2592 -10050.287 -7661.0282 214.06179 8.2635168e-24
103000 399.48144 323.14367 433.64948 2437.5232 -10099.345 -7661.8217 1414.3599 8.2635826e-24
104000 403.91297 352.82436 483.24961 2464.5631 -10128.039 -7663.4757 402.00008 8.2636057e-24
105000 399.44161 312.26084 493.93718 2437.2801 -10101.003 -7663.7228 504.67201 8.2636064e-24
106000 402.95299 308.09393 478.59661 2458.7056 -10121.59 -7662.8843 97.701725 8.2636229e-24
107000 392.07106 304.14376 438.71809 2392.3071 -10055.345 -7663.0381 252.79829 8.2636327e-24
108000 393.70287 346.41411 459.28468 2402.264 -10066.724 -7664.4599 887.00705 8.2636671e-24
109000 391.47643 308.81161 501.50488 2388.6788 -10052.91 -7664.2308 326.77367 8.2636442e-24
110000 403.70435 315.5849 464.09377 2463.2902 -10128.673 -7665.3827 -5.6251063 8.2635781e-24
111000 394.85248 346.14815 503.04687 2409.2785 -10074.267 -7664.9887 -138.63914 8.263596e-24
112000 399.46953 349.4274 430.61396 2437.4505 -10105.053 -7667.6029 446.93 8.2636098e-24
113000 390.96228 333.13036 421.74225 2385.5416 -10051.415 -7665.8736 1197.2272 8.2636064e-24
114000 400.87912 343.79219 479.14529 2446.0514 -10113.317 -7667.2661 375.41621 8.2636857e-24
115000 394.39043 352.97725 447.26251 2406.4592 -10073.998 -7667.5392 207.19142 8.263697e-24
116000 396.84629 318.40188 414.17025 2421.4442 -10089.19 -7667.7455 501.58224 8.263681e-24
117000 390.92085 356.0007 426.48853 2385.2888 -10052.827 -7667.5383 -111.31242 8.2636904e-24
118000 393.71794 318.11416 469.51592 2402.3559 -10070.578 -7668.2216 333.42163 8.2636139e-24
119000 386.65863 334.63961 495.60868 2359.282 -10026.953 -7667.6713 466.00594 8.2636047e-24
120000 393.75255 327.86854 479.21179 2402.5671 -10070.921 -7668.3536 340.30475 8.263651e-24
121000 387.80309 281.41022 450.15501 2366.2652 -10035.438 -7669.1728 416.934 8.2637149e-24
122000 398.51867 389.36572 476.41914 2431.6486 -10101.155 -7669.5067 918.52662 8.2637777e-24
123000 408.95841 322.05456 520.74629 2495.349 -10166.644 -7671.2955 607.79453 8.2637831e-24
124000 396.82158 333.96653 488.57211 2421.2934 -10092.448 -7671.1545 747.44253 8.2637656e-24
125000 408.21373 338.9252 413.6189 2490.8051 -10161.917 -7671.1115 681.44287 8.2637561e-24
126000 384.51254 345.26425 439.77203 2346.1871 -10016.103 -7669.9163 55.80732 8.2637973e-24
127000 390.61572 354.54614 450.29895 2383.427 -10054.196 -7670.7694 395.58452 8.2638544e-24
128000 399.44833 324.56533 496.24898 2437.3211 -10109.186 -7671.8653 963.77292 8.26387e-24
129000 395.85429 316.97239 446.65853 2415.3913 -10087.426 -7672.0345 291.35145 8.2638319e-24
130000 393.40547 300.69468 467.68308 2400.4493 -10072.857 -7672.4072 -86.167762 8.2638306e-24
131000 392.03156 313.24581 460.261 2392.0661 -10065.167 -7673.1004 214.13152 8.2638117e-24
132000 380.59567 329.56445 431.81798 2322.2875 -9994.182 -7671.8945 417.62073 8.2638313e-24
133000 387.06254 341.84713 470.43183 2361.7466 -10035.214 -7673.4679 -5.8037414 8.2638748e-24
134000 403.99279 356.33442 467.75422 2465.0501 -10139.298 -7674.2481 260.63529 8.263867e-24
135000 386.26735 385.65897 464.57944 2356.8945 -10029.872 -7672.977 1291.2327 8.2638485e-24
136000 403.95414 347.93908 417.90677 2464.8143 -10140.463 -7675.6484 -43.426037 8.2638353e-24
137000 394.34558 360.45758 448.55343 2406.1856 -10081.21 -7675.0247 503.6964 8.2638396e-24
138000 388.31235 345.91686 467.44594 2369.3725 -10045.237 -7675.8644 1070.1158 8.2638346e-24
139000 401.59974 332.04419 508.86419 2450.4484 -10127.61 -7677.1616 253.82278 8.2639234e-24
140000 402.39696 338.83859 467.61769 2455.3128 -10132.035 -7676.7218 1570.7305 8.2639306e-24
141000 404.42144 280.6012 498.80986 2467.6656 -10145.053 -7677.3871 -90.067587 8.2639046e-24
142000 394.0993 348.82557 492.20132 2404.6829 -10081.321 -7676.6386 439.2488 8.2639446e-24
143000 393.6602 347.91551 463.82284 2402.0036 -10080.279 -7678.2752 902.09681 8.2639502e-24
144000 403.2642 362.93262 480.6687 2460.6045 -10138.743 -7678.1386 298.12861 8.2639755e-24
145000 396.36698 332.10495 434.89429 2418.5196 -10097.254 -7678.7344 1022.3551 8.264009e-24
146000 395.07468 341.61125 465.54221 2410.6344 -10089.18 -7678.5454 551.60246 8.2640516e-24
147000 387.26415 327.56565 451.46115 2362.9767 -10042.022 -7679.0448 -62.778634 8.2640034e-24
148000 391.54986 319.52561 419.54523 2389.1269 -10067.218 -7678.091 -126.12178 8.2639722e-24
149000 388.52834 339.18554 449.81739 2370.6904 -10049.783 -7679.0931 295.10692 8.2639669e-24
150000 403.06234 353.16355 482.42445 2459.3728 -10140.073 -7680.7003 901.24113 8.2640098e-24
151000 401.4533 359.61123 497.31754 2449.5549 -10130.291 -7680.7363 134.50812 8.263968e-24
152000 398.53144 352.2869 443.42091 2431.7265 -10112.789 -7681.0622 858.7915 8.2639672e-24
153000 392.24486 359.21818 441.2996 2393.3676 -10073.53 -7680.1629 455.12746 8.2639968e-24
154000 385.18321 347.27959 419.21614 2350.2794 -10030.995 -7680.7153 600.66935 8.263991e-24
155000 400.42776 368.54411 470.45619 2443.2973 -10124.879 -7681.5816 704.87135 8.2640132e-24
156000 396.88154 351.39682 452.5791 2421.6593 -10104.116 -7682.4566 -464.21906 8.2639726e-24
157000 396.48998 342.35086 479.18347 2419.2701 -10101.475 -7682.2054 466.846 8.2639715e-24
158000 390.32349 330.55196 459.35293 2381.644 -10063.485 -7681.8407 31.483643 8.2640228e-24
159000 409.2442 365.98649 512.16123 2497.0927 -10180.988 -7683.8948 986.71988 8.2640339e-24
160000 387.49603 321.52831 444.60848 2364.3916 -10046.115 -7681.7234 684.79709 8.2640516e-24
161000 386.80818 296.37547 422.42232 2360.1945 -10042.838 -7682.6436 870.7098 8.2640553e-24
162000 396.54073 306.04178 460.46397 2419.5798 -10103.265 -7683.6854 433.74497 8.2641006e-24
163000 393.01413 353.3085 389.23134 2398.0614 -10081.864 -7683.8023 562.82481 8.2640802e-24
164000 393.10071 317.53156 491.4068 2398.5897 -10083.614 -7685.0245 337.02281 8.2640565e-24
165000 390.26334 310.66908 521.12915 2381.2769 -10066.318 -7685.0412 36.271315 8.2640722e-24
166000 399.44121 351.0389 480.76765 2437.2777 -10122.246 -7684.9682 753.78072 8.2640924e-24
167000 390.27513 330.73529 470.80529 2381.3489 -10067.253 -7685.9044 799.59421 8.2641285e-24
168000 405.09006 367.28599 513.32484 2471.7454 -10158.66 -7686.9144 513.3169 8.2641797e-24
169000 397.50323 337.17297 437.37188 2425.4527 -10111.847 -7686.3948 116.88194 8.2642197e-24
170000 397.37224 364.86808 436.71572 2424.6534 -10111.359 -7686.7056 -125.84875 8.2641627e-24
171000 387.90609 333.20748 478.91395 2366.8936 -10052.946 -7686.0525 754.59199 8.264175e-24
172000 398.15364 344.25345 463.22603 2429.4213 -10117.389 -7687.9682 455.98814 8.2641363e-24
173000 400.20766 340.45104 442.11215 2441.9543 -10130.615 -7688.6603 1070.672 8.264129e-24
174000 393.24037 358.04911 479.58537 2399.4419 -10087.748 -7688.3057 512.14451 8.2641206e-24
175000 399.18523 365.99034 442.06205 2435.7158 -10124.679 -7688.9632 1311.0037 8.2641303e-24
176000 390.69776 336.58721 442.64937 2383.9276 -10072.666 -7688.7383 514.02032 8.2640927e-24
177000 402.74763 348.21701 462.95034 2457.4525 -10147.915 -7690.4628 161.66974 8.2640693e-24
178000 398.72787 392.96016 495.40462 2432.9251 -10122.19 -7689.2649 256.62764 8.2640549e-24
179000 395.95492 296.92963 507.48741 2416.0054 -10105.931 -7689.9259 1253.9382 8.2640715e-24
180000 396.05703 372.81332 417.56908 2416.6284 -10107.629 -7691.0003 667.40732 8.2641629e-24
181000 391.33944 361.89332 447.21382 2387.843 -10079.067 -7691.2241 -57.39384 8.2641262e-24
182000 384.73681 326.86804 394.80715 2347.5556 -10037.697 -7690.1415 883.69878 8.2640876e-24
183000 389.43622 345.88945 480.34938 2376.23 -10067.679 -7691.4494 786.3316 8.2641703e-24
184000 385.75261 309.58079 484.30305 2353.7537 -10046.045 -7692.2909 904.09325 8.2641386e-24
185000 401.60537 333.83647 488.13418 2450.4828 -10143.764 -7693.2808 824.76058 8.2641768e-24
186000 402.03115 348.86838 473.88636 2453.0808 -10146.453 -7693.3726 643.21455 8.2641176e-24
187000 391.41099 332.38619 412.18869 2388.2796 -10081.201 -7692.9216 470.31163 8.2641658e-24
188000 387.37389 362.29235 456.00634 2363.6463 -10056.614 -7692.9674 1362.8544 8.2641145e-24
189000 395.18417 329.88599 471.14604 2411.3024 -10104.301 -7692.9982 295.27424 8.264106e-24
190000 399.34861 323.09574 505.0107 2436.7127 -10130.998 -7694.2858 788.39379 8.2641085e-24
191000 390.24422 379.95209 426.31198 2381.1603 -10074.716 -7693.5553 677.03804 8.2641705e-24
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

73
examples/HEAT/out.Elj_ehex Normal file
View File

@ -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

73
examples/HEAT/out.Elj_hex Normal file
View File

@ -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

68
examples/HEAT/out.Espce_ehex Normal file
View File

@ -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

68
examples/HEAT/out.Espce_hex Normal file
View File

@ -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

64
examples/HEAT/out.Tlj_ehex Normal file
View File

@ -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

64
examples/HEAT/out.Tlj_hex Normal file
View File

@ -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

64
examples/HEAT/out.Tspce_ehex Normal file
View File

@ -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

64
examples/HEAT/out.Tspce_hex Normal file
View File

@ -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

4
examples/README
View File

@ -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.