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[lammps-users] Friction coefient calculation getting error in thermo style
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[lammps-users] Friction coefient calculation getting error in thermo style

From: tanni bhattacharjee <tanni222byc@...24...>
Date: Mon, 10 Jul 2017 16:30:50 +0530

i want to calculate friction between water and graphite...
#LAMMPS Input file generated by Avogadro
# MD simulation for SPCE
units       real
variable    T equal 283.15     #86.4956
variable    V equal vol
variable    dt equal 1
variable    p equal 5000    # correlation length
variable    s equal 10      # sample interval
variable    d equal $p*$s   # dump interval

# convert from LAMMPS real units to SI

variable    kB equal 1.3806504e-23    # [J/K/** Boltzmann
variable    atm2Pa equal 101325.0
variable    A2m equal 1.0e-10
variable    fs2s equal 1.0e-15
variable    convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}

units real

atom_style full

dimension 3

boundary p p p

#The SPC/E water potential
pair_style      lj/cut/coul/long 12 12
kspace_style    ewald 1.0e-4
pair_coeff      1 1 0.15535 3.1533
pair_coeff      * 2 0.00000 0.0000
bond_style      harmonic
angle_style     harmonic
read_data      data.lammps
bond_coeff      1 100.00   1.000
angle_coeff     1 100.00 109.47
#special_bonds   lj/coul 0.0 0.0 0.5

group water type  2 3
group graphite type 1

neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes

timestep      ${dt}
thermo        $d
variable     v equal vol
print        "volume: $v"

fix             RigidOHBonds water shake 0.0001 20 0 b 1 a 1
fix   freeze graphite setforce 0.0 0.0 0.0

velocity       water create 260 4928459 rot yes mom yes dist gaussian
velocity       graphite create 260 4928459 dist gaussian
fix            ensemble water nvt temp $T $T 10 drag 0.2

compute tgraph graphite temp
compute twater water temp
thermo_style   custom step temp c_tgraph c_twater pe etotal press vol density
thermo         10

#unfix       NVT
fix         NVE all nve
reset_timestep 0
variable    p equal 1000    # correlation length
variable    s equal 2      # sample interval
variable    d equal $p*$s   # dump interval

compute         force  water group/group  graphite       
variable        fxy equal fxy
variable        fxz equal fxz
variable        fyz equal fyz

fix          SS all ave/correlate $s $p $d &
v_fxy v_fxz v_fyz type auto file vis.dat ave running
variable     scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
variable        la11 equal trap(f_SS[3])*${scale}
variable        la22 equal trap(f_SS[4])*${scale}
variable        la33 equal trap(f_SS[5])*${scale}
variable        la equal (v_la11+v_la22+v_la33)/3.0

variable     ndens equal count(all)/vol
thermo_style    custom step temp press v_fxy v_fxz v_fyz v_la11 v_la22 v_la33 v_la
print        "average frictioncoeffient"

# Run the simulation
run            900000