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 = 3.9946083 3.9946083 3.9946083 Created orthogonal box = (0.0000000 -45.894556 0.0000000) to (32.452352 45.894556 5.6492293) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8838322 6.2583485 5.6492293 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -45.894556 0.0000000) to (32.452352 45.894556 5.6492293) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8838322 6.2583485 5.6492293 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -45.894556 0.0000000) to (32.452352 45.894556 5.6492293) create_atoms CPU = 0.004 seconds 532 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 25 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 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_623376124862_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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3319.5678 0 -3319.5678 14113.333 79 0 -3462.8246 0 -3462.8246 -300.98755 Loop time of 3.87735 on 1 procs for 79 steps with 1056 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3319.56779791869 -3462.82144427581 -3462.82457074751 Force two-norm initial, final = 166.77495 0.11391532 Force max component initial, final = 35.164319 0.013628039 Final line search alpha, max atom move = 1.0000000 0.013628039 Iterations, force evaluations = 79 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8044 | 3.8044 | 3.8044 | 0.0 | 98.12 Neigh | 0.035884 | 0.035884 | 0.035884 | 0.0 | 0.93 Comm | 0.018152 | 0.018152 | 0.018152 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01896 | | | 0.49 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5314.00 ave 5314 max 5314 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: 138560.0 ave 138560 max 138560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138560 Ave neighs/atom = 131.21212 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3462.8246 0 -3462.8246 -300.98755 16827.769 81 0 -3462.8408 0 -3462.8408 -37.104634 16815.585 Loop time of 0.111014 on 1 procs for 2 steps with 1056 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 = -3462.82457074751 -3462.84014829297 -3462.84075903774 Force two-norm initial, final = 16.240357 0.76082717 Force max component initial, final = 10.176428 0.65861142 Final line search alpha, max atom move = 0.00027232550 0.00017935668 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10899 | 0.10899 | 0.10899 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044152 | 0.00044152 | 0.00044152 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001579 | | | 1.42 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223.00 ave 5223 max 5223 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: 138288.0 ave 138288 max 138288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138288 Ave neighs/atom = 130.95455 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3462.8408 0 -3462.8408 -37.104634 Loop time of 6.195e-06 on 1 procs for 0 steps with 1056 atoms 193.7% 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 | | 6.195e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223.00 ave 5223 max 5223 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: 138376.0 ave 138376 max 138376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138376 Ave neighs/atom = 131.03788 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 5.135 | 5.135 | 5.135 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 -3462.8408 -3462.8408 32.496682 91.69888 5.6429855 -37.104634 -37.104634 -24.181524 -62.690321 -24.442056 2.6210919 960.2156 Loop time of 7.127e-06 on 1 procs for 0 steps with 1056 atoms 238.5% 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 | | 7.127e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223.00 ave 5223 max 5223 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69188.0 ave 69188 max 69188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138376.0 ave 138376 max 138376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138376 Ave neighs/atom = 131.03788 Neighbor list builds = 0 Dangerous builds = 0 1056 -3462.84075903774 eV 2.62109192518375 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04