143 lines
4.7 KiB
Plaintext
143 lines
4.7 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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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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read_data data.1.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 &
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lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
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pair_modify tail no
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 none # CO-C CO-C
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pair_coeff 1 2 none # CO-C CD-
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pair_coeff 1 3 none # CO-C HD-
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pair_coeff 1 4 none # CO-C H1-H
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pair_coeff 1 5 none # CO-C OH-D
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pair_coeff 1 6 none # CO-C HO-D
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pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
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pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
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pair_coeff 2 2 none # CD- CD-
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pair_coeff 2 3 none # CD- HD-
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pair_coeff 2 4 none # CD- H1-H
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pair_coeff 2 5 none # CD- OH-D
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pair_coeff 2 6 none # CD- HO-D
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pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
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pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
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pair_coeff 3 3 none # HD- HD-
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pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
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pair_coeff 3 5 none # HD- OH-D
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pair_coeff 3 6 none # HD- HO-D
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pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
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pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
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pair_coeff 4 4 none # H1-H H1-H
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pair_coeff 4 5 none # H1-H OH-D
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pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
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pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
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pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
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pair_coeff 5 5 none # OH-D OH-D
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pair_coeff 5 6 none # OH-D HO-D
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pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
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pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
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pair_coeff 6 6 none # HO-D HO-D
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pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
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pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
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pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
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pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
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pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
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variable nsteps equal 2500000
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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 2 4 5 a 6
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
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run 250000
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reset_timestep 0
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variable lambda equal ramp(1.0,0.0)
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variable minusl equal 1.0-v_lambda
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variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
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variable q2 equal -0.180*(1.0-v_lambda)
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variable q3 equal 0.060*(1.0-v_lambda)
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variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
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variable q5 equal -0.683*v_lambda
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variable q6 equal 0.418*v_lambda
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fix fADAPT all adapt/fep 125000 &
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pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
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pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
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pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
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pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
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atom charge 1 v_q1 &
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atom charge 2 v_q2 &
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atom charge 3 v_q3 &
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atom charge 4 v_q4 &
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atom charge 5 v_q5 &
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atom charge 6 v_q6 &
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after yes
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variable dlambda equal -0.002
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variable minusdl equal 0.002
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variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
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variable dq2 equal 0.180*v_dlambda
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variable dq3 equal -0.060*v_dlambda
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variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
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variable dq5 equal -0.683*v_dlambda
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variable dq6 equal 0.418*v_dlambda
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compute cFEP all fep ${temp} &
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pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
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pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
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pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
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pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
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atom charge 1 v_dq1 &
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atom charge 2 v_dq2 &
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atom charge 3 v_dq3 &
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atom charge 4 v_dq4 &
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atom charge 5 v_dq5 &
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atom charge 6 v_dq6
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fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.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 C H H O H 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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