bff2e64bbc
I did NOT author this commit, I am only pushing it because for some reason, Github does not permit Aidan to do so Co-authored-by: Aidan Thompson <athomps@sandia.gov>
131 lines
4.7 KiB
Groff
131 lines
4.7 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-59-g16e0a7788a)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate calculation of Gaussian descriptors on a grid
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# for a cell with two atoms of type 1 and type 2.
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# The output in dump.glocal shows that for grid points
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# sitting on an atom of type 1 or 2:
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# val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219
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# val2 = 1.0/(0.2 *sqrt(2.0*pi))**3 = 7.93670
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# These values are extracted to the log file
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#
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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 ${nz}
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region box block 0 1 0 1 0 1
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create_box 2 box
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Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box basis 1 1 basis 2 2
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Created 2 atoms
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using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
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create_atoms CPU = 0.001 seconds
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mass * 180.88
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# define atom compute and grid compute
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variable rcutfac equal 4.67637
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variable radelem1 equal 0.5
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variable radelem2 equal 0.5
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variable sigmaelem1 equal 0.1355
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variable sigmaelem2 equal 0.2
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variable gaussian_options string "${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
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4.67637 ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}
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4.67637 0.5 ${radelem2} ${sigmaelem1} ${sigmaelem2}
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4.67637 0.5 0.5 ${sigmaelem1} ${sigmaelem2}
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4.67637 0.5 0.5 0.1355 ${sigmaelem2}
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4.67637 0.5 0.5 0.1355 0.2
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# build zero potential to force ghost atom creation
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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 mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${gaussian_options}
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compute mygridlocal all gaussian/grid/local grid 2 ${ngrid} ${ngrid} ${gaussian_options}
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compute mygridlocal all gaussian/grid/local grid 2 2 ${ngrid} ${gaussian_options}
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compute mygridlocal all gaussian/grid/local grid 2 2 2 ${gaussian_options}
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compute mygridlocal all gaussian/grid/local grid 2 2 2 4.67637 0.5 0.5 0.1355 0.2
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# define output
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dump 1 all local 1000 dump.glocal c_mygridlocal[*]
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dump 2 all custom 1000 dump.gatom id x y z
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compute val1 all reduce max c_mygridlocal[7] inputs local
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compute val2 all reduce max c_mygridlocal[8] inputs local
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thermo_style custom step c_val1 c_val2
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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 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 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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1 neighbor lists, perpetual/occasional/extra = 1 0 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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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
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Per MPI rank memory allocation (min/avg/max) = 3.522 | 3.523 | 3.524 Mbytes
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Step c_val1 c_val2
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0 25.521859 7.9367045
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Loop time of 2.238e-06 on 4 procs for 0 steps with 2 atoms
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89.4% CPU use with 4 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 | | 2.238e-06 | | |100.00
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Nlocal: 0.5 ave 1 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 274.5 ave 275 max 274 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 16 ave 40 max 0 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Total # of neighbors = 64
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Ave neighs/atom = 32
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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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