forked from lijiext/lammps
201 lines
7.9 KiB
Groff
201 lines
7.9 KiB
Groff
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LAMMPS (28 Jul 2021)
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# 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*${nrep}
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variable nrepx equal 3*1
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variable nrepy equal 2*${nrep}
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variable nrepy equal 2*1
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variable nrepz equal 1*${nrep}
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variable nrepz equal 1*1
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variable ngridx equal 3*${ngrid}
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variable ngridx equal 3*2
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variable ngridy equal 2*${ngrid}
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variable ngridy equal 2*2
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variable ngridz equal 1*${ngrid}
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variable ngridz equal 1*2
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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 nx equal 3
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variable ny equal ${nrepy}
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variable ny equal 2
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variable nz equal ${nrepz}
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variable nz equal 1
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boundary p p p
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lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
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lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1
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Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
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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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region box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
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region box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz}
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region box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz}
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region box prism 0 3 0 2 0 1 2 ${nz} ${nz}
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region box prism 0 3 0 2 0 1 2 1 ${nz}
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region box prism 0 3 0 2 0 1 2 1 1
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create_box 1 box
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Created triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
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WARNING: Triclinic box skew is large (src/domain.cpp:219)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 12 atoms
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using lattice units in triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000)
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create_atoms CPU = 0.001 seconds
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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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12 atoms in group snapgroup
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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 "${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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4.67637 ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 0.5 ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 0.5 1 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
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4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
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4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
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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_style zero 4.67637
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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 b all sna/atom 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
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compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
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compute mygrid all sna/grid grid 6 ${ngridy} ${ngridz} ${snap_options}
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compute mygrid all sna/grid grid 6 4 ${ngridz} ${snap_options}
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compute mygrid all sna/grid grid 6 4 2 ${snap_options}
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compute mygrid all sna/grid grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
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compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
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compute mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} ${snap_options}
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compute mygridlocal all sna/grid/local grid 6 4 ${ngridz} ${snap_options}
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compute mygridlocal all sna/grid/local grid 6 4 2 ${snap_options}
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compute mygridlocal all sna/grid/local grid 6 4 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
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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( (c_mygrid[13][4] - c_b[7][1])^2 + (c_mygrid[13][5] - c_b[7][2])^2 + (c_mygrid[13][6] - c_b[7][3])^2 + (c_mygrid[13][7] - c_b[7][4])^2 + (c_mygrid[13][8] - c_b[7][5])^2 )"
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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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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.67637
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ghost atom cutoff = 6.67637
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binsize = 3.338185, bins = 6 3 1
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4 neighbor lists, perpetual/occasional/extra = 1 3 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton/tri
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stencil: half/bin/3d/tri
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bin: standard
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(2) compute sna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(3) compute sna/grid, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(4) compute sna/grid/local, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 8.435 | 8.435 | 8.435 Mbytes
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Step v_B5atom v_B5grid v_rmse_global
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0 1.0427295 1.0427295 7.2262471e-14
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Loop time of 1e-06 on 1 procs for 0 steps with 12 atoms
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1e-06 | | |100.00
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Nlocal: 12.0000 ave 12 max 12 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 604.000 ave 604 max 604 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 384.000 ave 384 max 384 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 768.000 ave 768 max 768 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 768
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Ave neighs/atom = 64.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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