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lammps/examples/USER/dpd/dpdrx-shardlow/in.dpdrx.old
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# Example for running DPD-RX
log log.dpdrx
boundary p p p
units metal # ev, ps
atom_style dpd
atom_modify map array
#fix Concentrations all property/atom rx_rdx rx_hcn rx_no2 rx_no rx_h2o rx_n2 rx_h2 rx_co rx_co2 ghost yes
fix Concentrations all property/atom rx_rdx rx_h2 rx_no2 rx_n2 rx_hcn rx_no rx_h2o rx_co rx_co2 ghost yes
fix 4 all rx kinetics.dpdrx none lammps_rk4
#fix 4 all rx kinetics_null.dpdrx none lammps_rk4
#fix 4 all rx lammps_rk4 kinetics.dpdrx
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
region box block 0 6.0 0 6.0 0.0 6.0 units lattice
create_box 2 box
region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
create_atoms 1 region atoms
comm_modify mode single vel yes
mass * 222.12
#Set concentrations
set atom * d_rdx 1.00
set atom * d_h2 0.0
set atom * d_no2 0.0
set atom * d_n2 0.0
set atom * d_hcn 0.0
set atom * d_no 0.0
set atom * d_h2o 0.0
set atom * d_co 0.0
set atom * d_co2 0.0
#Set the internal temperature of the particles
set atom * dpd/theta 2065.00
#Set the kinetic temperature of the particles
velocity all create 2065.0 875661 dist gaussian
timestep 0.001
pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
pair_coeff * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
#fix 4 all rx lammps_rk4 kinetics.dpdrx
compute dpdU all dpd
compute dpdUatom all dpd/atom
compute crdx all property/atom d_rdx
variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
thermo 1
thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
thermo_modify format float %15.8f flush yes
dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
dump_modify 2 sort id
restart 10 restart.dpdrx
write_data data.dpdrx.initial
run 10
write_data data.dpdrx.final
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