Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/USER/hadress/H-AdResS/HADRESS_Water
2f5827189b3cefficient_neuronet

Last Change
Raw File

HADRESS_Water
View Options

# SPC/E water box benchmark
# This is HAdResS setup for simulation of water molecules.
# The water molecules are simulated and coupled into two resolution:
# High resolution in which atomistic SPC/E forcefields are present and
# Low resolution in which coarse-grained WCA forcefield is computed.
# For more information see Documentation and the follwoing paper:
# Heidari et al., Eur. Phys. J. Special Topics, 2016.
# You need to have the file "restart.waterT300.100" for running the script.
# Thus you need to run first the equillibration script (LongSetup) for 50000 timestep,
# and then set it as the restart file.
units real
atom_style full/hars
boundary p p p
#read_data HAdResS_SPC.data
read_restart restart.waterT300.50000
variable root index waterT300
variable Nrun equal 1000000
variable Nf equal 100
variable Ne equal 10
variable Nr equal ${Nf}/${Ne}
variable Ndump equal 500
variable Nrestart equal 10000
variable Nr_rdf equal 0.5*${Nrun}/${Ne}
variable Comp_AT_Size equal 60.0
variable Comp_HY_Size equal 25.0
variable Hyb_Shape string slab
variable Comp_Dens_nMolType equal 1
variable Comp_Pres_Switch equal 1
variable Comp_Pres_Start equal 150000
variable Comp_Pres_End equal 300000
variable Comp_Pres_Freq equal 1000
variable Comp_Pres_Lambda_Size equal 0.02
variable Comp_Dens_Switch equal 1
variable Comp_Dens_Start equal 500000
variable Comp_Dens_End equal 900000
variable Comp_Dens_Freq equal 1000
variable Comp_Dens_Alpha equal 4.0
variable Comp_Dens_Sigma equal 6.0
variable Comp_Dens_Range_Int equal 2.0
variable Comp_Dens_Bin_Size equal 1.5
variable Comp_Dens_Ref_Dens equal 0.1
variable Load_File_Flag equal 0
variable Text equal 300.0
variable Pext equal 1.0
pair_style hybrid/overlay lj/cut/hars/cg 2.469416506 0 0 lj/cut/coul/dsf/hars/at 0.2 10.0 12.0 0 0
pair_coeff * * lj/cut/hars/cg 1.0 2.2
pair_coeff 1 1 lj/cut/coul/dsf/hars/at 0.15535 3.166
pair_coeff * 2 lj/cut/coul/dsf/hars/at 0.0000 0.0000
pair_modify shift yes
#######################################################################
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
#special_bonds lj/cut/coul/dsf/hars/at 0.0 0.0 0.5
special_bonds lj/coul 0.0 0.0 0.5
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
fix LAMBDACALC all lambdah/calc ${Comp_Dens_nMolType} ${Comp_HY_Size} ${Comp_AT_Size} ${Comp_Pres_Switch} ${Comp_Pres_Lambda_Size} ${Comp_Pres_Freq} ${Comp_Pres_Start} ${Comp_Pres_End} ${Hyb_Shape} &
${Comp_Dens_Switch} ${Comp_Dens_Bin_Size} ${Comp_Dens_Freq} ${Comp_Dens_Start} ${Comp_Dens_End} ${Comp_Dens_Sigma} ${Comp_Dens_Range_Int} ${Comp_Dens_Ref_Dens} ${Comp_Dens_Alpha} ${Load_File_Flag}
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 3 all nve
fix 4 all langevin 300.0 300.0 100 9892571
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 5 1000 5000 x lower 3.0 v_Patom ave one file Pres.profile
fix DensityD all ave/spatial 5 1000 5000 x lower 3.0 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 ke ebond eangle evdwl ecoul etotal c_SumFFX c_SumFFY c_SumFFZ
thermo_modify flush yes
thermo ${Nf}
dump 2 all custom 500 wat.lammpstrj id type x y z vx vy vz
restart ${Nrestart} restart.${root}
run ${Nrun}
c4science · Help