Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/USER/hadress/Relaxation/LongSetup
7d1c34b5098defficient_neuronet

Last Change
Raw File

LongSetup
View Options

# SPC/E water box benchmark
# HAdResS Relaxation Setup
# Maziar Heidari, Max Planck Institute for Polymer Research
# (heidari@mpip-mainz.mpg.de))
units real
atom_style full/hars
boundary p p p
#read_data HAdResS_SPC.data
#read_restart restart.waterT300.10000
variable root index waterT300
variable Nrun equal 50000
variable Nf equal 100
variable Ne equal 10
variable Nr equal ${Nf}/${Ne}
variable Ndump equal 1000
variable Nrestart equal 10000
variable Nr_rdf equal 0.5*${Nrun}/${Ne}
variable Text equal 300.0
variable Pext equal 1.0
variable x index 1
variable y index 1
variable z index 1
variable xx equal 40*$x
variable yy equal 8*$y
variable zz equal 8*$z
variable half_xx equal 0.5*${xx}
variable half_yy equal 0.5*${yy}
variable half_zz equal 0.5*${zz}
#######################################################################
molecule mol1 molecule
lattice fcc 5.0
region box block -${half_xx} ${half_xx} -${half_yy} ${half_yy} -${half_zz} ${half_zz}
create_box 2 box bond/types 1 extra/bond/per/atom 2 angle/types 1 extra/angle/per/atom 1 dihedral/types 0 improper/types 0 extra/special/per/atom 2
create_atoms 0 box mol mol1 10
mass 1 15.9994
mass 2 1.00794
pair_style lj/cut/coul/dsf 0.2 10.0 12.0
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
########################################################################
bond_style harmonic
angle_style harmonic
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all npt temp ${Text} ${Text} 100.0 iso ${Pext} ${Pext} 1000.0
velocity all create 300 432567 dist uniform
timestep 1.0
########################################################################
compute FFX all property/atom fx
compute SumFFX all reduce sum c_FFX
compute FFY all property/atom fy
compute SumFFY all reduce sum c_FFY
compute FFZ all property/atom fz
compute SumFFZ all reduce sum c_FFZ
compute T all temp
fix TempAve all ave/time ${Ne} ${Nr} ${Nf} c_T
compute Pperatom all stress/atom NULL
variable Patom atom -1.0*c_Pperatom[1]/(3*0.5*(yhi-ylo)*(zhi-zlo))
variable P equal press
fix PressAve all ave/time ${Ne} ${Nr} ${Nf} v_P
fix PressureP all ave/spatial 10 1000 10000 x lower 1.0 v_Patom ave one file Pres.profile
fix DensityD all ave/spatial 10 1000 10000 x lower 1.0 density/number ave one file Dens.profile
compute rdf all rdf 100 1 1 # oxygen-oxygen
fix rdf all ave/time 10 1000 10000 c_rdf file O.rdf mode vector
########################################################################
thermo_style custom step temp f_TempAve press f_PressAve density vol ke ebond eangle evdwl ecoul etotal c_SumFFX c_SumFFY c_SumFFZ
thermo_modify flush yes
thermo ${Nf}
dump trj all atom ${Ndump} wat.lammpstrj
restart ${Nrestart} restart.${root}
run ${Nrun}
c4science · Help