90 lines
2.5 KiB
Plaintext
90 lines
2.5 KiB
Plaintext
# created by fftool
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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special_bonds lj/coul 0.0 0.0 0.5
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read_data data.0.lmp
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# read_restart restart.*.lmp
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# reset_timestep 0
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pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
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pair_modify tail yes
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 none # C-CF C-CF
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pair_coeff 1 2 none # C-CF H-D
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pair_coeff 1 3 none # C-CF FD-
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pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # C-CF Hw
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pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # C-CF Ow
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pair_coeff 2 2 none # H-D H-D
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pair_coeff 2 3 none # H-D FD-
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pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 1.0 # H-D Hw
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pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
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pair_coeff 3 3 none # FD- FD-
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pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 0.0 # FD- Hw
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pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 0.0 # FD- Ow
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pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
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pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
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pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
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variable nsteps equal 500000
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variable nprint equal ${nsteps}/500
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variable ndump equal ${nsteps}/100
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# variable nrestart equal ${nsteps}/10
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variable temp equal 300.0
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variable press equal 1.0
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neighbor 2.0 bin
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timestep 2.0
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velocity all create ${temp} 12345
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thermo_style multi
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thermo ${nprint}
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fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
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run 200000
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reset_timestep 0
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variable dlambda equal 1.0
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variable minusdl equal -1.0
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variable dqC equal 0.48*v_dlambda-0.24*(1.0-v_dlambda)
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variable dqH equal 0.06*(1.0-v_dlambda)
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variable dqF equal -0.12*v_dlambda
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compute cFEP all fep ${temp} &
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pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
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pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
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atom charge 1 v_dqC &
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atom charge 2 v_dqH &
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atom charge 3 v_dqF
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fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
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# compute cRDF all rdf 100 1 1
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# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
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# compute cMSD all msd
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# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
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dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify dCONF element C H F H O
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# restart ${nrestart} restart.*.lmp
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run ${nsteps}
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# write_restart restart.*.lmp
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write_data data.*.lmp
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