Diffusion lammps (efficient_neuronet) Browse

in.spce_ehex
576c6315c7f1efficient_neuronet

in.spce_ehex
View Options

			###############################################################################
			#
			#
			# 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_vcmxv_vcmx+v_vcmyv_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}

lammps/examples/HEAT/in.spce_ehex576c6315c7f1efficient_neuronet

in.spce_ehexView Options

lammps/examples/HEAT/in.spce_ehex
576c6315c7f1efficient_neuronet

in.spce_ehex
View Options