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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -39.060003 0.0000000) to (13.020001 39.060003 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0076927 5.0076927 3.6110986 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.060003 0.0000000) to (13.020001 39.060003 3.6110986) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0076927 5.0076927 3.6110986 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.060003 0.0000000) to (13.020001 39.060003 3.6110986) create_atoms CPU = 0.001 seconds 158 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 = 5 27 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 2 atoms, new total = 312 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_321233176498_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 = 5 27 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) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1284.1572 0 -1284.1572 34926.921 18 0 -1318.0983 0 -1318.0983 7761.025 Loop time of 0.917402 on 1 procs for 18 steps with 312 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 = -1284.15715518499 -1318.09744720335 -1318.09829537363 Force two-norm initial, final = 89.312247 0.093779354 Force max component initial, final = 31.275483 0.027944566 Final line search alpha, max atom move = 1.0000000 0.027944566 Iterations, force evaluations = 18 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91318 | 0.91318 | 0.91318 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021509 | 0.0021509 | 0.0021509 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002075 | | | 0.23 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2784.00 ave 2784 max 2784 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: 24268.0 ave 24268 max 24268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24268 Ave neighs/atom = 77.782051 Neighbor list builds = 0 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 = 5 27 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -1318.0983 0 -1318.0983 7761.025 3672.9298 33 0 -1318.3295 0 -1318.3295 -3.6162503 3689.3165 Loop time of 0.450915 on 1 procs for 15 steps with 312 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 = -1318.09829537363 -1318.32840000066 -1318.32951819602 Force two-norm initial, final = 39.182963 0.49206658 Force max component initial, final = 30.837377 0.091696289 Final line search alpha, max atom move = 0.00083085389 7.6186218e-05 Iterations, force evaluations = 15 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44641 | 0.44641 | 0.44641 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095216 | 0.00095216 | 0.00095216 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003551 | | | 0.79 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2784.00 ave 2784 max 2784 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: 24152.0 ave 24152 max 24152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24152 Ave neighs/atom = 77.410256 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 = 5 27 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1318.3295 0 -1318.3295 -3.6162503 Loop time of 6.075e-06 on 1 procs for 0 steps with 312 atoms 164.6% 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 | | 6.075e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2784.00 ave 2784 max 2784 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: 24152.0 ave 24152 max 24152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24152 Ave neighs/atom = 77.410256 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 = 5 27 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) = 4.564 | 4.564 | 4.564 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 -1318.3295 -1318.3295 12.901115 78.022284 3.6652196 -3.6162503 -3.6162503 -20.0079 -20.102316 29.261465 2.2967255 135.73749 Loop time of 6.785e-06 on 1 procs for 0 steps with 312 atoms 221.1% 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 | | 6.785e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2784.00 ave 2784 max 2784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12076.0 ave 12076 max 12076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24152.0 ave 24152 max 24152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24152 Ave neighs/atom = 77.410256 Neighbor list builds = 0 Dangerous builds = 0 312 -1318.32951819602 eV 2.2967254949629 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01