mirror of https://github.com/lammps/lammps.git
90 lines
1.5 KiB
Plaintext
90 lines
1.5 KiB
Plaintext
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# Tethered nanorods
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atom_style molecular
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read_data data.rigid.tnr
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# Specify bond parameters
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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special_bonds fene
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# Specify initial velocities
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velocity all create 1.4 109345
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# Specify rigid components
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group rods type 2
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group tethers subtract all rods
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neigh_modify exclude molecule rods delay 0 every 1
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# Specify the pair potentials
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pair_style lj/cut 2.5
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pair_modify shift yes
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pair_coeff * * 1.0 1.0 1.122
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pair_coeff 2 2 1.0 1.0 2.5
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# Specify output
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thermo 100
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thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
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thermo_modify flush yes lost warn
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timestep 0.005
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log log.tnr
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fix 1 rods rigid molecule
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fix 2 tethers nve
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fix 3 all langevin 1.4 1.4 1.0 437624
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run 5000
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# Replace fix rigid and fix langevin with new ones
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unfix 1
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unfix 3
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fix 3 tethers langevin 1.4 1.4 1.0 198450
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# Test different integrators for rods
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fix 1 rods rigid/nve molecule
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print "rigid/nve"
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run 1000
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unfix 1
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fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
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print "rigid/nvt"
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run 1000
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unfix 1
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compute myTemp all temp
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fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 &
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dilate all
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print "rigid/npt iso"
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fix_modify 1 temp myTemp
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run 1000
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unfix 1
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fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
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print "rigid/npt x"
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run 1000
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unfix 1
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fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
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print "rigid/nph iso"
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run 1000
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unfix 1
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fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 &
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couple xy dilate all
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print "rigid/nph xy couple"
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run 1000
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