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>
69 lines
1.6 KiB
Plaintext
69 lines
1.6 KiB
Plaintext
# 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 ny equal ${nrep}
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variable nz equal ${nrep}
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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 0 1 0 &
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a3 0 0 1 &
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basis 0 0 0 &
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basis 0.5 0.5 0.5 &
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 2 box
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create_atoms 1 box basis 1 1 basis 2 2
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mass * 180.88
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# define atom compute and grid compute
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variable rcutfac equal 4.67637
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variable radelem1 equal 0.5
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variable radelem2 equal 0.5
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variable sigmaelem1 equal 0.1355
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variable sigmaelem2 equal 0.2
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variable gaussian_options string &
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"${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
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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_coeff * *
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# define atom and grid computes
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compute mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
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${gaussian_options}
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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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