666de878ad
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10558 f3b2605a-c512-4ea7-a41b-209d697bcdaa
97 lines
2.2 KiB
Plaintext
97 lines
2.2 KiB
Plaintext
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
|