48 lines
1.5 KiB
Plaintext
48 lines
1.5 KiB
Plaintext
# LAMMPS Input File for Grain Boundaries
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# Mark Tschopp, Dec2009
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# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS
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# This file will generate a single Sigma5(310) STGB and run PTM
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# ---------- Initialize Simulation ---------------------
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clear
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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 atomic
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# ---------- Create Sigma5(310) Structure ---------
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lattice fcc 4.05
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region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box
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create_box 2 whole
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region upper block INF INF 0.000000 64.0361225 INF INF units box
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lattice fcc 4.05 orient x 0 3 1 orient y 0 -1 3 orient z 1 0 0
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create_atoms 1 region upper
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region lower block INF INF -64.0361225 0.000000 INF INF units box
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lattice fcc 4.05 orient x 0 3 -1 orient y 0 1 3 orient z 1 0 0
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create_atoms 2 region lower
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group upper type 1
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group lower type 2
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mass 1 1.0
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mass 2 1.0
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# ---------- Define Interatomic Potential ---------------------
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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pair_coeff 1 1 1 1.1 2.8
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# ---------- Displace atoms and delete overlapping atoms ---------------------
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displace_atoms upper move 0 0 0 units lattice
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delete_atoms overlap 0.35 lower upper
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# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) -------------------
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compute ptm all ptm/atom default 0.1
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# ---------- Dump data into Data file -------------
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reset_timestep 0
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dump 1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7]
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dump_modify 1 element Al Al
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run 1
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print "All done"
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