Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/HEAT/in.spce_hex
7d77aea42d30lammm-devel

Last Change
Raw File

in.spce_hex
View Options

###############################################################################
#
#
# 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}
c4science · Help