forked from lijiext/lammps
160 lines
6.5 KiB
Groff
160 lines
6.5 KiB
Groff
LAMMPS (2 Jun 2022)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate calculation of SNAP bispectrum descriptors on a grid
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# CORRECTNESS: The two atom positions coincide with two of
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# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
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# The same is true for compute grid/local c_mygridlocal[8][4-11].
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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
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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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units metal
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atom_modify map hash
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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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 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
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lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
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Lattice spacing in x,y,z = 3.316 3.316 3.316
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 1 box
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Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 2 atoms
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using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
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create_atoms CPU = 0.000 seconds
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mass 1 180.88
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# define atom compute and grid compute
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group snapgroup type 1
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2 atoms in group snapgroup
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quadratic equal 0
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variable switch equal 1
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variable snap_options string "${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 ${ngrid} ${ngrid} ${ngrid} ${snap_options}
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compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options}
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compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options}
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compute mygrid all sna/grid grid 2 2 2 ${snap_options}
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compute mygrid all sna/grid grid 2 2 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 ${ngrid} ${ngrid} ${ngrid} ${snap_options}
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compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options}
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compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options}
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compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options}
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compute mygridlocal all sna/grid/local grid 2 2 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[2][5]
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variable B5grid equal c_mygrid[8][8]
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variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][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 c_mygridlocal[*]
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dump 2 all custom 1000 dump.batom id x y z c_b[*]
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# run
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run 0
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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 = 1 1 1
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2 neighbor lists, perpetual/occasional/extra = 1 1 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/atomonly/newton
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stencil: half/bin/3d
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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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Per MPI rank memory allocation (min/avg/max) = 7.127 | 7.127 | 7.127 Mbytes
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Step v_B5atom v_B5grid v_rmse_global
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0 1.0427295 1.0427295 9.1551336e-16
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Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms
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139.9% CPU use with 1 MPI tasks x 1 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 | | 1.43e-06 | | |100.00
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Nlocal: 2 ave 2 max 2 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 339 ave 339 max 339 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 64 ave 64 max 64 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 128
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Ave neighs/atom = 64
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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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