294 lines
11 KiB
Groff
294 lines
11 KiB
Groff
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate bispectrum computes
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 2
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variable a equal 2.0
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units metal
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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 2
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variable ny equal ${nrep}
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variable ny equal 2
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variable nz equal ${nrep}
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variable nz equal 2
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc 2
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Lattice spacing in x,y,z = 2 2 2
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 2 0 ${ny} 0 ${nz}
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region box block 0 2 0 2 0 ${nz}
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region box block 0 2 0 2 0 2
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create_box 2 box
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Created orthogonal box = (0 0 0) to (4 4 4)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 16 atoms
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using lattice units in orthogonal box = (0 0 0) to (4 4 4)
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create_atoms CPU = 0.001 seconds
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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Displacing atoms ...
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# set up dummy potential to satisfy cutoff
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variable rcutfac equal 6.0
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pair_style zero ${rcutfac}
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pair_style zero 6
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pair_coeff * *
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# set up per-atom computes
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compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta
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**************** Begin of POD Potentials ****************
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species: Ta
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periodic boundary conditions: 1 1 1
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number of environment clusters: 1
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number of principal compoments: 2
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inner cut-off radius: 1
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outer cut-off radius: 5
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bessel polynomial degree: 3
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inverse polynomial degree: 6
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one-body potential: 1
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two-body radial basis functions: 6
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three-body radial basis functions: 5
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three-body angular degree: 4
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four-body radial basis functions: 0
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four-body angular degree: 0
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five-body radial basis functions: 0
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five-body angular degree: 0
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six-body radial basis functions: 0
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six-body angular degree: 0
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seven-body radial basis functions: 0
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seven-body angular degree: 0
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number of local descriptors per element for one-body potential: 1
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number of local descriptors per element for two-body potential: 6
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number of local descriptors per element for three-body potential: 25
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number of local descriptors per element for four-body potential: 0
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number of local descriptors per element for five-body potential: 0
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number of local descriptors per element for six-body potential: 0
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number of local descriptors per element for seven-body potential: 0
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number of local descriptors per element for all potentials: 32
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number of global descriptors: 32
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**************** End of POD Potentials ****************
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**************** Begin of Model Coefficients ****************
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total number of coefficients for POD potential: 32
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total number of elements for PCA projection matrix: 0
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total number of elements for PCA centroids: 0
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**************** End of Model Coefficients ****************
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compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta
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**************** Begin of POD Potentials ****************
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species: Ta
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periodic boundary conditions: 1 1 1
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number of environment clusters: 1
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number of principal compoments: 2
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inner cut-off radius: 1
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outer cut-off radius: 5
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bessel polynomial degree: 3
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inverse polynomial degree: 6
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one-body potential: 1
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two-body radial basis functions: 6
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three-body radial basis functions: 5
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three-body angular degree: 4
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four-body radial basis functions: 0
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four-body angular degree: 0
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five-body radial basis functions: 0
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five-body angular degree: 0
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six-body radial basis functions: 0
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six-body angular degree: 0
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seven-body radial basis functions: 0
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seven-body angular degree: 0
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number of local descriptors per element for one-body potential: 1
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number of local descriptors per element for two-body potential: 6
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number of local descriptors per element for three-body potential: 25
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number of local descriptors per element for four-body potential: 0
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number of local descriptors per element for five-body potential: 0
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number of local descriptors per element for six-body potential: 0
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number of local descriptors per element for seven-body potential: 0
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number of local descriptors per element for all potentials: 32
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number of global descriptors: 32
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**************** End of POD Potentials ****************
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**************** Begin of Model Coefficients ****************
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total number of coefficients for POD potential: 32
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total number of elements for PCA projection matrix: 0
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total number of elements for PCA centroids: 0
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**************** End of Model Coefficients ****************
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# set up compute snap generating global array
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compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta
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**************** Begin of POD Potentials ****************
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species: Ta
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periodic boundary conditions: 1 1 1
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number of environment clusters: 1
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number of principal compoments: 2
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inner cut-off radius: 1
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outer cut-off radius: 5
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bessel polynomial degree: 3
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inverse polynomial degree: 6
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one-body potential: 1
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two-body radial basis functions: 6
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three-body radial basis functions: 5
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three-body angular degree: 4
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four-body radial basis functions: 0
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four-body angular degree: 0
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five-body radial basis functions: 0
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five-body angular degree: 0
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six-body radial basis functions: 0
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six-body angular degree: 0
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seven-body radial basis functions: 0
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seven-body angular degree: 0
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number of local descriptors per element for one-body potential: 1
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number of local descriptors per element for two-body potential: 6
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number of local descriptors per element for three-body potential: 25
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number of local descriptors per element for four-body potential: 0
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number of local descriptors per element for five-body potential: 0
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number of local descriptors per element for six-body potential: 0
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number of local descriptors per element for seven-body potential: 0
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number of local descriptors per element for all potentials: 32
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number of global descriptors: 32
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**************** End of POD Potentials ****************
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**************** Begin of Model Coefficients ****************
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total number of coefficients for POD potential: 32
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total number of elements for PCA projection matrix: 0
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total number of elements for PCA centroids: 0
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**************** End of Model Coefficients ****************
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#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
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compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta
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**************** Begin of POD Potentials ****************
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species: Ta
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periodic boundary conditions: 1 1 1
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number of environment clusters: 1
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number of principal compoments: 2
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inner cut-off radius: 1
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outer cut-off radius: 5
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bessel polynomial degree: 3
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inverse polynomial degree: 6
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one-body potential: 1
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two-body radial basis functions: 6
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three-body radial basis functions: 5
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three-body angular degree: 4
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four-body radial basis functions: 0
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four-body angular degree: 0
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five-body radial basis functions: 0
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five-body angular degree: 0
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six-body radial basis functions: 0
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six-body angular degree: 0
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seven-body radial basis functions: 0
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seven-body angular degree: 0
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number of local descriptors per element for one-body potential: 1
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number of local descriptors per element for two-body potential: 6
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number of local descriptors per element for three-body potential: 25
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number of local descriptors per element for four-body potential: 0
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number of local descriptors per element for five-body potential: 0
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number of local descriptors per element for six-body potential: 0
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number of local descriptors per element for seven-body potential: 0
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number of local descriptors per element for all potentials: 32
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number of global descriptors: 32
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**************** End of POD Potentials ****************
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**************** Begin of Model Coefficients ****************
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total number of coefficients for POD potential: 32
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total number of elements for PCA projection matrix: 0
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total number of elements for PCA centroids: 0
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**************** End of Model Coefficients ****************
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#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
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#dump mydump_ld all custom 1000 dump_ld id c_ld[*]
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#dump mydump_dd all custom 1000 dump_dd id c_dd[*]
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variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor
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fix ldprint all print 1 "${sample_ld1}"
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run ${nsteps}
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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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WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87)
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WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87)
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WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87)
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WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89)
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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 = 8
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ghost atom cutoff = 8
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binsize = 4, bins = 1 1 1
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5 neighbor lists, perpetual/occasional/extra = 1 4 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 pod/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 podd/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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(4) compute pod/gdd, 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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(5) compute pod/ldd, 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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0.344594831165384
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Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 0 0 0 0
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Loop time of 1.207e-06 on 1 procs for 0 steps with 16 atoms
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165.7% 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 | | 1.207e-06 | | |100.00
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Nlocal: 16 ave 16 max 16 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1984 ave 1984 max 1984 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4311 ave 4311 max 4311 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 8623 ave 8623 max 8623 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 8623
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Ave neighs/atom = 538.9375
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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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