115 lines
2.9 KiB
Plaintext
115 lines
2.9 KiB
Plaintext
# Demonstrate calculation of SNAP bispectrum
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# descriptors on a grid for triclinic cell
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# This triclinic cell has 6 times the volume of the single
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# unit cell used by in.grid
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# and contains 12 atoms. It is a 3x2x1 supercell
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# with each unit cell containing 2 atoms and the
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# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
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# The grid is listed in x-fastest order
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# CORRECTNESS: The atom positions coincide with certain
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# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8]
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# and c_b[7][1-5] should match c_mygrid[13][4-8].
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# Local arrays can not be access directly in the script,
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# but they are printed out to file dump.blocal.tri
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# Initialize simulation
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variable nrep index 1
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variable a index 3.316
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variable ngrid index 2
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variable nrepx equal 3*${nrep}
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variable nrepy equal 2*${nrep}
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variable nrepz equal 1*${nrep}
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variable ngridx equal 3*${ngrid}
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variable ngridy equal 2*${ngrid}
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variable ngridz equal 1*${ngrid}
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units metal
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atom_modify map hash sort 0 0
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrepx}
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variable ny equal ${nrepy}
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variable nz equal ${nrepz}
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boundary p p p
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lattice custom $a &
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a1 1 0 0 &
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a2 1 1 0 &
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a3 1 1 1 &
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basis 0 0 0 &
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basis 0.0 0.0 0.5 &
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spacing 1 1 1
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box tilt large
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region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# define atom compute and grid compute
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group snapgroup type 1
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quadratic equal 0
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variable switch equal 1
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variable snap_options string &
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"${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} quadraticflag ${quadratic} &
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bzeroflag ${bzero} switchflag ${switch}"
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# build zero potential to satisfy compute sna/atom
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pair_style zero ${rcutfac}
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pair_coeff * *
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# define atom and grid computes
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compute b all sna/atom ${snap_options}
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compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} &
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${snap_options}
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compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} &
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${snap_options}
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# define output
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variable B5atom equal c_b[7][5]
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variable B5grid equal c_mygrid[13][8]
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# do not compare x,y,z because assignment of ids
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# to atoms is not unnique for different processor grids
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variable rmse_global equal "sqrt( &
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(c_mygrid[13][4] - c_b[7][1])^2 + &
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(c_mygrid[13][5] - c_b[7][2])^2 + &
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(c_mygrid[13][6] - c_b[7][3])^2 + &
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(c_mygrid[13][7] - c_b[7][4])^2 + &
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(c_mygrid[13][8] - c_b[7][5])^2 &
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)"
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thermo_style custom step v_B5atom v_B5grid v_rmse_global
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# this is the only way to view the local grid
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dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*]
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dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]
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# run
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run 0
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