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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -46.317289 0.0000000) to (32.751269 46.317289 5.1463654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0650498 6.2900022 5.1463654 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -46.317289 0.0000000) to (32.751269 46.317289 5.1463654) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0650498 6.2900022 5.1463654 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -46.317289 0.0000000) to (32.751269 46.317289 5.1463654) create_atoms CPU = 0.005 seconds 650 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1292 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_748636486270_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4041.9588 0 -4041.9588 70591.605 48 0 -4412.5006 0 -4412.5006 -1077.2303 Loop time of 2.00918 on 1 procs for 48 steps with 1292 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 = -4041.95883721952 -4412.4963977638 -4412.50055488559 Force two-norm initial, final = 867.93996 0.16857664 Force max component initial, final = 287.85927 0.017297665 Final line search alpha, max atom move = 1.0000000 0.017297665 Iterations, force evaluations = 48 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.917 | 1.917 | 1.917 | 0.0 | 95.41 Neigh | 0.063606 | 0.063606 | 0.063606 | 0.0 | 3.17 Comm | 0.015253 | 0.015253 | 0.015253 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01327 | | | 0.66 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8306.00 ave 8306 max 8306 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: 227316.0 ave 227316 max 227316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227316 Ave neighs/atom = 175.94118 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.476 | 5.476 | 5.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -4412.5006 0 -4412.5006 -1077.2303 15613.558 50 0 -4412.5099 0 -4412.5099 -4.9078985 15601.861 Loop time of 0.155484 on 1 procs for 2 steps with 1292 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4412.5005548856 -4412.50773705711 -4412.50986359568 Force two-norm initial, final = 21.855561 0.83283795 Force max component initial, final = 16.275341 0.57098855 Final line search alpha, max atom move = 0.00011936943 6.8158575e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15111 | 0.15111 | 0.15111 | 0.0 | 97.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003369 | | | 2.17 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8280.00 ave 8280 max 8280 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: 227016.0 ave 227016 max 227016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227016 Ave neighs/atom = 175.70898 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.614 | 5.614 | 5.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4412.5099 0 -4412.5099 -4.9078985 Loop time of 6.395e-06 on 1 procs for 0 steps with 1292 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8280.00 ave 8280 max 8280 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: 227056.0 ave 227056 max 227056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227056 Ave neighs/atom = 175.73994 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.614 | 5.614 | 5.614 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 -4412.5099 -4412.5099 32.766526 92.586084 5.142808 -4.9078985 -4.9078985 -15.722424 58.6049 -57.606171 2.3488627 492.16508 Loop time of 8.399e-06 on 1 procs for 0 steps with 1292 atoms 226.2% 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 | | 8.399e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8280.00 ave 8280 max 8280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113528.0 ave 113528 max 113528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227056.0 ave 227056 max 227056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227056 Ave neighs/atom = 175.73994 Neighbor list builds = 0 Dangerous builds = 0 1292 -4412.50986359568 eV 2.34886265604639 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02