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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5820674 5.5248139 6.0992294 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.911290 0.0000000) to (31.100090 35.911290 6.0992294) create_atoms CPU = 0.001 seconds 627 atoms in group lower Displacing atoms ... 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1245 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_876687166519_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5106.9561 0 -5106.9561 81232.344 100 0 -5501.3204 0 -5501.3204 11129.722 Loop time of 11.214 on 1 procs for 100 steps with 1245 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5106.95613416047 -5501.31532279708 -5501.32042859856 Force two-norm initial, final = 497.38508 0.28771543 Force max component initial, final = 145.73197 0.066725087 Final line search alpha, max atom move = 0.71742480 0.047870233 Iterations, force evaluations = 100 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.164 | 11.164 | 11.164 | 0.0 | 99.55 Neigh | 0.026296 | 0.026296 | 0.026296 | 0.0 | 0.23 Comm | 0.0101 | 0.0101 | 0.0101 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01405 | | | 0.13 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4989.00 ave 4989 max 4989 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: 110222.0 ave 110222 max 110222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110222 Ave neighs/atom = 88.531727 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -5501.3204 0 -5501.3204 11129.722 13623.78 107 0 -5501.9366 0 -5501.9366 166.89128 13703.74 Loop time of 0.519317 on 1 procs for 7 steps with 1245 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 = -5501.32042859857 -5501.93314840368 -5501.93663844228 Force two-norm initial, final = 202.70603 2.8100853 Force max component initial, final = 184.55238 2.0919301 Final line search alpha, max atom move = 0.00011724872 0.00024527613 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51677 | 0.51677 | 0.51677 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037441 | 0.00037441 | 0.00037441 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002177 | | | 0.42 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4983.00 ave 4983 max 4983 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: 110174.0 ave 110174 max 110174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110174 Ave neighs/atom = 88.493173 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5501.9366 0 -5501.9366 166.89128 Loop time of 2.317e-06 on 1 procs for 0 steps with 1245 atoms 172.6% 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 | | 2.317e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4983.00 ave 4983 max 4983 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: 109674.0 ave 109674 max 109674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109674 Ave neighs/atom = 88.091566 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.173 | 5.173 | 5.173 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 -5501.9366 -5501.9366 31.128888 72.284706 6.0901655 166.89128 166.89128 55.703712 200.75501 244.21511 2.2284024 866.62226 Loop time of 2.428e-06 on 1 procs for 0 steps with 1245 atoms 205.9% 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 | | 2.428e-06 | | |100.00 Nlocal: 1245.00 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4983.00 ave 4983 max 4983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54837.0 ave 54837 max 54837 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109674.0 ave 109674 max 109674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109674 Ave neighs/atom = 88.091566 Neighbor list builds = 0 Dangerous builds = 0 1245 -5501.93663844228 eV 2.22840235940602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12