LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-179-g353121c942-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Demonstrate bispectrum computes # initialize simulation variable nsteps index 0 variable nrep equal 2 variable a equal 2.0 units metal # generate the box and atom positions using a BCC lattice variable nx equal ${nrep} variable nx equal 2 variable ny equal ${nrep} variable ny equal 2 variable nz equal ${nrep} variable nz equal 2 boundary p p p atom_modify map hash lattice bcc $a lattice bcc 2 Lattice spacing in x,y,z = 2 2 2 region box block 0 ${nx} 0 ${ny} 0 ${nz} region box block 0 2 0 ${ny} 0 ${nz} region box block 0 2 0 2 0 ${nz} region box block 0 2 0 2 0 2 create_box 2 box Created orthogonal box = (0 0 0) to (4 4 4) 1 by 1 by 1 MPI processor grid create_atoms 2 box Created 16 atoms using lattice units in orthogonal box = (0 0 0) to (4 4 4) create_atoms CPU = 0.001 seconds mass * 180.88 displace_atoms all random 0.1 0.1 0.1 123456 Displacing atoms ... # set up dummy potential to satisfy cutoff variable rcutfac equal 6.0 pair_style zero ${rcutfac} pair_style zero 6 pair_coeff * * # set up per-atom computes compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 number of environment clusters: 1 number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 two-body radial basis functions: 6 three-body radial basis functions: 5 three-body angular degree: 4 four-body radial basis functions: 0 four-body angular degree: 0 five-body radial basis functions: 0 five-body angular degree: 0 six-body radial basis functions: 0 six-body angular degree: 0 seven-body radial basis functions: 0 seven-body angular degree: 0 number of local descriptors per element for one-body potential: 1 number of local descriptors per element for two-body potential: 6 number of local descriptors per element for three-body potential: 25 number of local descriptors per element for four-body potential: 0 number of local descriptors per element for five-body potential: 0 number of local descriptors per element for six-body potential: 0 number of local descriptors per element for seven-body potential: 0 number of local descriptors per element for all potentials: 32 number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Model Coefficients **************** total number of coefficients for POD potential: 32 total number of elements for PCA projection matrix: 0 total number of elements for PCA centroids: 0 **************** End of Model Coefficients **************** compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 number of environment clusters: 1 number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 two-body radial basis functions: 6 three-body radial basis functions: 5 three-body angular degree: 4 four-body radial basis functions: 0 four-body angular degree: 0 five-body radial basis functions: 0 five-body angular degree: 0 six-body radial basis functions: 0 six-body angular degree: 0 seven-body radial basis functions: 0 seven-body angular degree: 0 number of local descriptors per element for one-body potential: 1 number of local descriptors per element for two-body potential: 6 number of local descriptors per element for three-body potential: 25 number of local descriptors per element for four-body potential: 0 number of local descriptors per element for five-body potential: 0 number of local descriptors per element for six-body potential: 0 number of local descriptors per element for seven-body potential: 0 number of local descriptors per element for all potentials: 32 number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Model Coefficients **************** total number of coefficients for POD potential: 32 total number of elements for PCA projection matrix: 0 total number of elements for PCA centroids: 0 **************** End of Model Coefficients **************** # set up compute snap generating global array compute gdd all pod/global Ta_param.pod Ta_coefficients.pod Ta Ta **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 number of environment clusters: 1 number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 two-body radial basis functions: 6 three-body radial basis functions: 5 three-body angular degree: 4 four-body radial basis functions: 0 four-body angular degree: 0 five-body radial basis functions: 0 five-body angular degree: 0 six-body radial basis functions: 0 six-body angular degree: 0 seven-body radial basis functions: 0 seven-body angular degree: 0 number of local descriptors per element for one-body potential: 1 number of local descriptors per element for two-body potential: 6 number of local descriptors per element for three-body potential: 25 number of local descriptors per element for four-body potential: 0 number of local descriptors per element for five-body potential: 0 number of local descriptors per element for six-body potential: 0 number of local descriptors per element for seven-body potential: 0 number of local descriptors per element for all potentials: 32 number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Model Coefficients **************** total number of coefficients for POD potential: 32 total number of elements for PCA projection matrix: 0 total number of elements for PCA centroids: 0 **************** End of Model Coefficients **************** #fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector compute ldd all pod/local Ta_param.pod Ta_coefficients.pod Ta Ta **************** Begin of POD Potentials **************** species: Ta periodic boundary conditions: 1 1 1 number of environment clusters: 1 number of principal compoments: 2 inner cut-off radius: 1 outer cut-off radius: 5 bessel polynomial degree: 3 inverse polynomial degree: 6 one-body potential: 1 two-body radial basis functions: 6 three-body radial basis functions: 5 three-body angular degree: 4 four-body radial basis functions: 0 four-body angular degree: 0 five-body radial basis functions: 0 five-body angular degree: 0 six-body radial basis functions: 0 six-body angular degree: 0 seven-body radial basis functions: 0 seven-body angular degree: 0 number of local descriptors per element for one-body potential: 1 number of local descriptors per element for two-body potential: 6 number of local descriptors per element for three-body potential: 25 number of local descriptors per element for four-body potential: 0 number of local descriptors per element for five-body potential: 0 number of local descriptors per element for six-body potential: 0 number of local descriptors per element for seven-body potential: 0 number of local descriptors per element for all potentials: 32 number of global descriptors: 32 **************** End of POD Potentials **************** **************** Begin of Model Coefficients **************** total number of coefficients for POD potential: 32 total number of elements for PCA projection matrix: 0 total number of elements for PCA centroids: 0 **************** End of Model Coefficients **************** #fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector #dump mydump_ld all custom 1000 dump_ld id c_ld[*] #dump mydump_dd all custom 1000 dump_dd id c_dd[*] variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor fix ldprint all print 1 "${sample_ld1}" run ${nsteps} run 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87) WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87) WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87) WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89) Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 1 1 1 5 neighbor lists, perpetual/occasional/extra = 1 4 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (2) compute pod/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute podd/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (4) compute pod/global, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (5) compute pod/local, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard 0.344594831165384 Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 0 0 0 0 Loop time of 1.23e-06 on 1 procs for 0 steps with 16 atoms 243.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.23e-06 | | |100.00 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1984 ave 1984 max 1984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4311 ave 4311 max 4311 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8623 ave 8623 max 8623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8623 Ave neighs/atom = 538.9375 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00