forked from lijiext/lammps
80 lines
3.2 KiB
Plaintext
80 lines
3.2 KiB
Plaintext
## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
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variable x_rep equal 2 #x-direction replication number
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variable y_rep equal 2 #y-direction replication number
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variable z_rep equal 2 #z-direction replication number
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variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
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variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
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variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
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variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
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variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
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## This part defines units, alpha-quartz crystal, and atomic information
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#General
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units metal
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dimension 3
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boundary p p p
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atom_style charge
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#Lattice
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lattice custom 1.0 &
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a1 4.916000 0.000000 0.000000 &
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a2 -2.45800 4.257381 0.000000 &
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a3 0.000000 0.000000 5.405400 &
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&
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basis 0.469700 0.000000 0.000000 &
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basis 0.000000 0.469700 0.666667 &
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basis 0.530300 0.530300 0.333333 &
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&
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basis 0.413500 0.266900 0.119100 &
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basis 0.266900 0.413500 0.547567 &
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basis 0.733100 0.146600 0.785767 &
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basis 0.586500 0.853400 0.214233 &
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basis 0.853400 0.586500 0.452433 &
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basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
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#Computational Cell
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region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
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create_box 2 orthorhombic_unit_cell
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create_atoms 1 box &
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basis 1 1 &
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basis 2 1 &
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basis 3 1 &
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basis 4 2 &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2 &
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basis 9 2
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replicate ${x_rep} ${y_rep} ${z_rep}
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#Atomic Information
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mass 1 28.085500
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mass 2 15.999400
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set type 1 charge +2.4
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set type 2 charge -1.2
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## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
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#Pair Potentials
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pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
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pair_coeff 1 1 0.0 1.0 0.0
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pair_coeff 1 2 18003.757200 0.205205 133.538100
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pair_coeff 2 2 1388.773000 0.362319 175.000000
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pair_modify shift yes
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kspace_style pppm 1.0e-4
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#Neighbor style
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neighbor 2.0 bin
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neigh_modify check yes every 1 delay 0 page 100000 one 2000
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## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
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variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
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fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} #NPH does the time integration
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fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
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thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
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thermo 100
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run 20000 # 20 ps
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unfix quartz_qtb
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unfix scapegoat_qtb
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