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lammps/examples/USER/atc/molecule/in.water
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in.water
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log water.log
variable nstepsequil equal 500000
variable nsteps equal 1000#2500000
variable temp equal 300.0
variable tdamp equal 0.100
variable x_dim equal 20
variable y_dim equal 20
variable z_fluid equal 30
variable efieldz equal -5
variable seed equal 868026
variable x_max equal ${x_dim}/2
variable y_max equal ${y_dim}/2
variable fluid_half_thickness equal ${z_fluid}/2
#variable zmaxatc equal ${fluid_half_thickness}
#variable zmaxsub equal ${zmaxatc}-0.1
#variable zmaxsup equal ${zmaxatc}+0.1
units metal
atom_style full
dimension 3
newton off
neighbor 2 bin
neigh_modify every 1 delay 3 check yes
boundary p p p
kspace_style pppm 1e-4
pair_style lj/cut/coul/long 13.0 9.0
bond_style harmonic
angle_style harmonic
#read_data waterbox.dat # for equilibration
read_data water.init
lattice sc 0.05
region ATC block EDGE EDGE EDGE EDGE EDGE EDGE units box
#variable nelem equal round(2*${zmaxatc}/0.05)
variable nelem equal 1
group water type 1 2
group hyd type 1
group oxy type 2
timestep 0.0005
thermo 100
thermo_style custom step temp epair emol etotal press
dielectric 1.0
pair_coeff 1 * 0.0 0.0
pair_coeff 2 2 0.006596 3.1507
bond_coeff 1 19.513855 0.957200
angle_coeff 1 2.385027 104.519997
special_bonds amber
# assign SHAKE fixes
##fix 1 water shake 0.01 3 0 b 1 a 1
#velocity all create 0.0 1 rot yes dist uniform # for equilibration
variable dumpfreq equal 100
dump 1 all atom 500 waterequil.dump
dump_modify 1 image yes scale no flush yes
fix 2 all nvt temp ${temp} ${temp} ${tdamp}
fix press_avetime all ave/time 10 1 10 c_thermo_press ave running file pressdata.log
#run ${nstepsequil}
fix efield all efield 0. 0. v_efieldz
#run ${nstepsequil}
unfix 2
#fix 3 all nve
fix AtC all atc species_electrostatic water.mat
fix_modify AtC mesh create 1 1 ${nelem} ATC p p p
fix_modify AtC atom_element_map eulerian ${dumpfreq}
fix_modify AtC internal_quadrature off
fix_modify AtC atom_weight multiscale
fix_modify AtC add_species Hyd type 1
fix_modify AtC add_species Oxy type 2
fix_modify AtC add_molecule small Water water
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic short_range off
fix_modify AtC output waterFE ${dumpfreq} text binary
run ${nsteps}
#write_restart water.restart # for equilibration
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