76 lines
1.4 KiB
Plaintext
76 lines
1.4 KiB
Plaintext
# Simple virus model.
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#
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units lj
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dimension 3
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boundary f f f
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atom_style angle
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pair_style lj/cut 4.0
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pair_modify shift yes
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bond_style harmonic
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angle_style harmonic
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neigh_modify binsize 5.0
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read_data init.data
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group NC type 1
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group rest type 2 3 4
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group CA type 3
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timestep 0.0001
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variable R equal "ramp(v_R0,v_R1)"
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variable RF equal ${R1}
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variable Rw equal "v_RF - 0.5"
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print "**** R scales from ${R0} to ${R1} and wall is at ${Rw} ****"
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variable rr atom "sqrt( x*x + y*y + z*z )"
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compute ravg CA reduce ave v_rr
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region my_sphere sphere 0 0 0 v_Rw side out
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fix wall all wall/region my_sphere lj126 1.0 1.0 1.1225
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variable U equal pe
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variable epair equal epair
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fix U all ave/time 2000 1 2000 v_U v_R v_epair
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variable t equal time
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variable ravg equal c_ravg
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variable T equal 0.25
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variable pU equal f_U[1]
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variable pE equal f_U[3]
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fix out all print 2000 "$t ${pU} $R ${ravg} ${pE}" file thermo.${DATA}.dat screen no
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fix step1 rest nvt temp $T $T 1.0
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fix step2 NC nvt/manifold/rattle 1e-4 10 sphere v_R temp $T $T 1.0
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special_bonds lj 0 0 0
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angle_coeff 1 250.0 180.0
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thermo_style custom time step pe v_pU ke etotal epair temp v_R
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thermo 10000
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compute pe all pe/atom
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fix pe_avg all ave/atom 100 50 5000 c_pe
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dump traj_all all custom 5000 virus.dump id type x y z f_pe_avg
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run 2500000
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unfix out
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fix step1 rest nvt temp $T $T 1.0
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fix step2 NC nvt/manifold/rattle 1e-4 10 sphere ${R1} temp $T $T 1.0
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run 1000000
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