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 -56.364123 0.0000000) to (28.182061 56.364123 3.7004859) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8589761 4.8589761 3.7004859 Created 463 atoms using lattice units in orthogonal box = (0.0000000 -56.364123 0.0000000) to (28.182061 56.364123 3.7004859) create_atoms CPU = 0.002 seconds 463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8589761 4.8589761 3.7004859 Created 465 atoms using lattice units in orthogonal box = (0.0000000 -56.364123 0.0000000) to (28.182061 56.364123 3.7004859) create_atoms CPU = 0.002 seconds 465 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 42 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 = 928 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 42 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) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1198.3646 0 -1198.3646 51539.142 117 0 -1385.389 0 -1385.389 1037.969 Loop time of 0.83362 on 1 procs for 117 steps with 928 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 = -1198.36460293012 -1385.38778835389 -1385.38903114021 Force two-norm initial, final = 371.96499 0.13124220 Force max component initial, final = 90.985707 0.022729497 Final line search alpha, max atom move = 1.0000000 0.022729497 Iterations, force evaluations = 117 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76886 | 0.76886 | 0.76886 | 0.0 | 92.23 Neigh | 0.017556 | 0.017556 | 0.017556 | 0.0 | 2.11 Comm | 0.022572 | 0.022572 | 0.022572 | 0.0 | 2.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02463 | | | 2.95 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4712.00 ave 4712 max 4712 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: 50014.0 ave 50014 max 50014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50014 Ave neighs/atom = 53.894397 Neighbor list builds = 2 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 42 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 : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -1385.389 0 -1385.389 1037.969 11756.127 121 0 -1385.4416 0 -1385.4416 -111.05913 11768.31 Loop time of 0.0244612 on 1 procs for 4 steps with 928 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1385.38903114021 -1385.44136164825 -1385.44160306491 Force two-norm initial, final = 28.990992 1.6723497 Force max component initial, final = 26.351606 1.2308180 Final line search alpha, max atom move = 0.00044365249 0.00054605548 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021658 | 0.021658 | 0.021658 | 0.0 | 88.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005678 | 0.0005678 | 0.0005678 | 0.0 | 2.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002235 | | | 9.14 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4712.00 ave 4712 max 4712 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: 50072.0 ave 50072 max 50072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50072 Ave neighs/atom = 53.956897 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 42 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) = 4.696 | 4.696 | 4.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1385.4416 0 -1385.4416 -111.05913 Loop time of 6.285e-06 on 1 procs for 0 steps with 928 atoms 190.9% 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 | | 6.285e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4712.00 ave 4712 max 4712 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: 50088.0 ave 50088 max 50088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50088 Ave neighs/atom = 53.974138 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 42 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) = 4.696 | 4.696 | 4.696 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 -1385.4416 -1385.4416 28.177008 112.50564 3.7123157 -111.05913 -111.05913 -167.53758 -148.73317 -16.906643 2.3137901 191.38818 Loop time of 6.735e-06 on 1 procs for 0 steps with 928 atoms 237.6% 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 | | 6.735e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4712.00 ave 4712 max 4712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25044.0 ave 25044 max 25044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50088.0 ave 50088 max 50088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50088 Ave neighs/atom = 53.974138 Neighbor list builds = 0 Dangerous builds = 0 928 -1385.44160306491 eV 2.31379005978757 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01