LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -53.493117 0.0000000) to (43.676947 53.493117 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3848291 5.1294770 5.9028292 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -53.493117 0.0000000) to (43.676947 53.493117 8.8542437) create_atoms CPU = 0.007 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3848291 5.1294770 5.9028292 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.493117 0.0000000) to (43.676947 53.493117 8.8542437) create_atoms CPU = 0.007 seconds 1757 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 39 4 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_887933271505_003#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 39 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.222 | 5.222 | 5.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11232.435 0 -11232.435 64810.442 36 0 -12398.763 0 -12398.763 5831.5064 Loop time of 3.03026 on 1 procs for 36 steps with 3506 atoms 72.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -11232.4346218281 -12398.7626625908 -12398.7626625908 Force two-norm initial, final = 1023.6624 0.54023652 Force max component initial, final = 221.33021 0.10652990 Final line search alpha, max atom move = 3.7405439e-08 3.9847977e-09 Iterations, force evaluations = 36 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9397 | 2.9397 | 2.9397 | 0.0 | 97.01 Neigh | 0.037009 | 0.037009 | 0.037009 | 0.0 | 1.22 Comm | 0.023286 | 0.023286 | 0.023286 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03031 | | | 1.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7379.00 ave 7379 max 7379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190468.0 ave 190468 max 190468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190468 Ave neighs/atom = 54.326298 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 39 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.222 | 5.222 | 5.222 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -12398.763 0 -12398.763 5831.5064 41374.394 39 0 -12398.941 0 -12398.941 2879.8477 41462.292 Loop time of 1.59813 on 1 procs for 3 steps with 3506 atoms 73.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -12398.7626625909 -12398.9411235962 -12398.9411235962 Force two-norm initial, final = 261.39871 129.80910 Force max component initial, final = 158.59887 81.400980 Final line search alpha, max atom move = 7.3223498e-13 5.9604645e-11 Iterations, force evaluations = 3 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5377 | 1.5377 | 1.5377 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010999 | 0.010999 | 0.010999 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04942 | | | 3.09 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7383.00 ave 7383 max 7383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191294.0 ave 191294 max 191294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191294 Ave neighs/atom = 54.561894 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 39 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.359 | 5.359 | 5.359 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12398.941 0 -12398.941 2879.8477 Loop time of 6.485e-06 on 1 procs for 0 steps with 3506 atoms 169.6% 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 | | 6.485e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7383.00 ave 7383 max 7383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191200.0 ave 191200 max 191200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191200 Ave neighs/atom = 54.535083 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 39 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.359 | 5.359 | 5.359 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -12398.941 -12398.941 43.704644 107.06647 8.8607854 2879.8477 2879.8477 2423.133 3147.8373 3068.5727 2.2561028 1789.2812 Loop time of 6.775e-06 on 1 procs for 0 steps with 3506 atoms 265.7% 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 | | 6.775e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7383.00 ave 7383 max 7383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95600.0 ave 95600 max 95600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191200.0 ave 191200 max 191200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191200 Ave neighs/atom = 54.535083 Neighbor list builds = 0 Dangerous builds = 0 3506 -12398.9411235962 eV 2.25610284323301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05