variable T equal 293.15 # Simulated Temperature [K] variable V equal vol # Volume variable dt equal 1.0 # TimeStep in Femtosecond variable p equal 400 # Correlation Length in nanometers variable s equal 5 # Sample Interval variable d equal $p*$s # Dump output Interval variable srate equal 12.03 # SHEAR STRAIN RATE ################################################################################################# #CONVERT TO SI-UNITS variable kB equal 1.3806504e-23 # [J/K/** Boltzmann] Boltzmann Constant variable eV2J equal 1.6021764E-19 # eV energy unit to Joules variable kCal2J equal 4186.0/6.02214e23 variable atm2Pa equal 101325.0 # Atmospheric to Pascal Pressure units variable A2m equal 1.0e-10 # Atomic Mass Unit to Molecular Mass units variable fs2s equal 1.0e-15 variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m} ################################################################################################# units real atom_style sphere #atom_modify first big dimension 3 boundary p p p # create big particles with 3 different types and diameters lattice fcc 10 region box prism 0 20 0 15 0 10 0.0 0.0 0.0 create_box 4 box create_atoms 4 region box #group big type 4 set group all type/fraction 1 0.05 394895 set group all type/fraction 2 0.05 989894 set group all type/fraction 3 0.05 654379 #group big type 1 4 3 group CM1 type 1 group CM2 type 2 group CM3 type 3 group CM4 type 4 #set type 1 diameter 4 #density 12.5 #set type 2 diameter 3 #density 10.0 #set type 3 diameter 2 #density 7.5 #set type 4 diameter 1 #density 5.0 set type 1 mass 1090.00 set type 2 mass 750.00 set type 3 mass 500.00 set type 4 mass 250.00 set group CM1 density 100 set group CM2 density 100 set group CM3 density 100 set group CM2 density 100 velocity all create $T 102486 mom yes rot yes dist gaussian # equilibrate big particles, repulsive only to prevent aggregation variable sigma_CM1 equal 4.0 #20 variable sigma_CM2 equal 3.0 #15 variable sigma_CM3 equal 2.0 #10 variable sigma_CM4 equal 1.0 #05 variable cut1 equal 2.5*${sigma_CM1} variable cut2 equal 2.5*${sigma_CM2} variable cut3 equal 2.5*${sigma_CM3} variable cut4 equal 2.5*${sigma_CM4} variable cut11 equal 2.5*((${sigma_CM1}+${sigma_CM1})/2) variable cut12 equal 2.5*((${sigma_CM1}+${sigma_CM2})/2) variable cut13 equal 2.5*((${sigma_CM1}+${sigma_CM3})/2) variable cut14 equal 2.5*((${sigma_CM1}+${sigma_CM4})/2) variable cut22 equal 2.5*((${sigma_CM2}+${sigma_CM2})/2) variable cut23 equal 2.5*((${sigma_CM2}+${sigma_CM3})/2) variable cut24 equal 2.5*((${sigma_CM2}+${sigma_CM4})/2) variable cut33 equal 2.5*((${sigma_CM3}+${sigma_CM3})/2) variable cut34 equal 2.5*((${sigma_CM3}+${sigma_CM4})/2) variable cut44 equal 2.5*((${sigma_CM4}+${sigma_CM4})/2) pair_style lj/cut 2.5 pair_coeff * * 1 1 pair_coeff 1 1 3.107E-3 4.00 ${cut11} pair_coeff 1 2 2.715E-3 3.50 ${cut12} pair_coeff 1 3 2.325E-3 3.00 ${cut13} pair_coeff 1 4 1.941E-3 2.50 ${cut14} pair_coeff 2 2 2.330E-3 3.00 ${cut22} pair_coeff 2 3 1.941E-3 2.50 ${cut23} pair_coeff 2 4 1.552E-3 2.00 ${cut24} pair_coeff 3 3 1.553E-3 2.00 ${cut33} pair_coeff 3 4 1.164E-3 1.50 ${cut34} pair_coeff 4 4 0.775E-3 1.0 ${cut44} neighbor 0.3 bin neigh_modify delay 0 every 1 check yes #page 500000 one 50000 fix 1 all nve fix 2 all langevin $T $T 10.0 768012 dump 1 all xyz 1000 colloid_brownian.xyz timestep ${dt} thermo 1000 thermo_style custom step temp pe ke etotal vol press density lx ly lz run 100000 unfix 1 unfix 2 undump 1 reset_timestep 0 dump 3 all xyz 1000 colloid_triclinic.xyz velocity all scale $T variable xyrate equal v_srate/ly # shear rate defined relative to perpendicular dimension variable xyrate equal ${srate}/ly fix 1 all nvt/sllod temp $T $T 10.0 fix 2 all deform 1 xy erate ${xyrate} remap v compute layers all chunk/atom bin/1d y center 0.05 units reduced fix 3 all ave/chunk 20 250 5000 layers vx file profile.nemd.3d-${srate} #compute temp after deforming box compute usual all temp compute tilt all temp/deform thermo 1000 thermo_style custom step temp c_usual pe etotal press vol density pxy thermo_modify temp tilt run 100000 # data gathering run variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt} variable visc equal -pxy/v_xyrate*${scale} fix vave all ave/time 10 100 1000 v_visc ave running file visc-avg-${srate} thermo 5000 thermo_style custom step temp c_usual pe etotal press vol density pxy v_visc f_vave thermo_modify temp tilt run 500000