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 = 3.7004859 3.7004859 3.7004859 Created orthogonal box = (0.0000000 -57.803438 0.0000000) to (28.901719 57.803438 3.7004859) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2117854 5.2117854 3.7004859 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -57.803438 0.0000000) to (28.901719 57.803438 3.7004859) create_atoms CPU = 0.003 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2117854 5.2117854 3.7004859 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -57.803438 0.0000000) to (28.901719 57.803438 3.7004859) create_atoms CPU = 0.002 seconds 490 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 43 2 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_857282754307_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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1403.8037 0 -1403.8037 20726.302 113 0 -1468.0692 0 -1468.0692 2581.7399 Loop time of 0.848065 on 1 procs for 113 steps with 978 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1403.80374060216 -1468.06793246217 -1468.0691962563 Force two-norm initial, final = 75.672558 0.12778442 Force max component initial, final = 28.634273 0.037396375 Final line search alpha, max atom move = 1.0000000 0.037396375 Iterations, force evaluations = 113 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79529 | 0.79529 | 0.79529 | 0.0 | 93.78 Neigh | 0.0083733 | 0.0083733 | 0.0083733 | 0.0 | 0.99 Comm | 0.020031 | 0.020031 | 0.020031 | 0.0 | 2.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02438 | | | 2.87 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4172.00 ave 4172 max 4172 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: 52968.0 ave 52968 max 52968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52968 Ave neighs/atom = 54.159509 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -1468.0692 0 -1468.0692 2581.7399 12364.202 118 0 -1468.2059 0 -1468.2059 -117.98325 12394.041 Loop time of 0.0339654 on 1 procs for 5 steps with 978 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1468.06919625631 -1468.20541091916 -1468.20587047867 Force two-norm initial, final = 62.084324 1.8583315 Force max component initial, final = 49.026881 1.7027006 Final line search alpha, max atom move = 0.00029383667 0.00050031589 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030452 | 0.030452 | 0.030452 | 0.0 | 89.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068391 | 0.00068391 | 0.00068391 | 0.0 | 2.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00283 | | | 8.33 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4140.00 ave 4140 max 4140 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: 52804.0 ave 52804 max 52804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52804 Ave neighs/atom = 53.991820 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.702 | 4.702 | 4.702 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1468.2059 0 -1468.2059 -117.98325 Loop time of 6.695e-06 on 1 procs for 0 steps with 978 atoms 194.2% 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 | | 6.695e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4151.00 ave 4151 max 4151 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: 52756.0 ave 52756 max 52756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52756 Ave neighs/atom = 53.942740 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.702 | 4.702 | 4.702 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 -1468.2059 -1468.2059 28.817639 115.92189 3.7101295 -117.98325 -117.98325 -71.400852 -220.70772 -61.841167 2.3528186 99.063341 Loop time of 6.404e-06 on 1 procs for 0 steps with 978 atoms 281.1% 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 | | 6.404e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4151.00 ave 4151 max 4151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26378.0 ave 26378 max 26378 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52756.0 ave 52756 max 52756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52756 Ave neighs/atom = 53.942740 Neighbor list builds = 0 Dangerous builds = 0 978 -1468.20587047867 eV 2.35281861821533 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01