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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9111318 4.8617724 4.0498230 Created 203 atoms using lattice units in orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) create_atoms CPU = 0.001 seconds 203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9111318 4.8617724 4.0498230 Created 205 atoms using lattice units in orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) create_atoms CPU = 0.001 seconds 205 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 ghost atom cutoff = 6 binsize = 3, bins = 6 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 408 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1667.5612 0 -1667.5612 54510.449 88 0 -1741.4522 0 -1741.4522 7724.9312 Loop time of 1.74606 on 1 procs for 88 steps with 408 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 = -1667.56122963966 -1741.45047549371 -1741.4522031112 Force two-norm initial, final = 123.88530 0.14445694 Force max component initial, final = 27.405295 0.032947821 Final line search alpha, max atom move = 1.0000000 0.032947821 Iterations, force evaluations = 88 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7344 | 1.7344 | 1.7344 | 0.0 | 99.33 Neigh | 0.004306 | 0.004306 | 0.004306 | 0.0 | 0.25 Comm | 0.0039562 | 0.0039562 | 0.0039562 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003445 | | | 0.20 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2585.00 ave 2585 max 2585 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: 26286.0 ave 26286 max 26286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26286 Ave neighs/atom = 64.426471 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -1741.4522 0 -1741.4522 7724.9312 4790.6374 93 0 -1741.5431 0 -1741.5431 166.25842 4811.5542 Loop time of 0.0772194 on 1 procs for 5 steps with 408 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 = -1741.4522031112 -1741.54284926703 -1741.54313164131 Force two-norm initial, final = 46.057048 1.0934052 Force max component initial, final = 40.738496 0.87288783 Final line search alpha, max atom move = 0.00044860876 0.00039158513 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076425 | 0.076425 | 0.076425 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013826 | 0.00013826 | 0.00013826 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006562 | | | 0.85 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2460.00 ave 2460 max 2460 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: 26280.0 ave 26280 max 26280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26280 Ave neighs/atom = 64.411765 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 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1741.5431 0 -1741.5431 166.25842 Loop time of 1.697e-06 on 1 procs for 0 steps with 408 atoms 176.8% 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 | | 1.697e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2448.00 ave 2448 max 2448 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: 26252.0 ave 26252 max 26252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26252 Ave neighs/atom = 64.343137 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 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.579 | 4.579 | 4.579 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 -1741.5431 -1741.5431 16.715953 71.128787 4.046773 166.25842 166.25842 211.95286 291.83143 -5.0090105 2.3028535 282.24107 Loop time of 1.513e-06 on 1 procs for 0 steps with 408 atoms 198.3% 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 | | 1.513e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2448.00 ave 2448 max 2448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13126.0 ave 13126 max 13126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26252.0 ave 26252 max 26252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26252 Ave neighs/atom = 64.343137 Neighbor list builds = 0 Dangerous builds = 0 408 -1741.54313164131 eV 2.30285347167158 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02