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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -57.843155 0.0000000) to (11.807185 57.843155 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3669021 5.2584687 5.8134559 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.843155 0.0000000) to (11.807185 57.843155 8.7201838) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3669021 5.2584687 5.8134559 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.843155 0.0000000) to (11.807185 57.843155 8.7201838) create_atoms CPU = 0.001 seconds 530 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 30 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.103 | 5.103 | 5.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4301.3145 0 -4301.3145 62994.605 108 0 -4628.9765 0 -4628.9765 12668.596 Loop time of 1.96798 on 1 procs for 108 steps with 1056 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4301.31452260924 -4628.97325696837 -4628.97650435329 Force two-norm initial, final = 627.79187 0.31893853 Force max component initial, final = 156.31113 0.079824657 Final line search alpha, max atom move = 1.0000000 0.079824657 Iterations, force evaluations = 108 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9352 | 1.9352 | 1.9352 | 0.0 | 98.34 Neigh | 0.011044 | 0.011044 | 0.011044 | 0.0 | 0.56 Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0105 | | | 0.53 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6638.00 ave 6638 max 6638 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: 184932.0 ave 184932 max 184932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184932 Ave neighs/atom = 175.12500 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -4628.9765 0 -4628.9765 12668.596 11911.157 117 0 -4629.5508 0 -4629.5508 128.42132 11980.046 Loop time of 0.103731 on 1 procs for 9 steps with 1056 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 = -4628.97650435329 -4629.55057006694 -4629.55083032652 Force two-norm initial, final = 185.24504 2.4564390 Force max component initial, final = 165.81547 1.7349470 Final line search alpha, max atom move = 0.00028587762 0.00049598253 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10056 | 0.10056 | 0.10056 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056148 | 0.00056148 | 0.00056148 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002614 | | | 2.52 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911.00 ave 6911 max 6911 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: 184912.0 ave 184912 max 184912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184912 Ave neighs/atom = 175.10606 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.242 | 5.242 | 5.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4629.5508 0 -4629.5508 128.42132 Loop time of 1.798e-06 on 1 procs for 0 steps with 1056 atoms 166.9% 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 | | 1.798e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6915.00 ave 6915 max 6915 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: 184700.0 ave 184700 max 184700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184700 Ave neighs/atom = 174.90530 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.242 | 5.242 | 5.242 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 -4629.5508 -4629.5508 11.785794 116.60983 8.7169482 128.42132 128.42132 -51.73513 233.87902 203.12007 2.308926 441.28755 Loop time of 2.348e-06 on 1 procs for 0 steps with 1056 atoms 212.9% 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 | | 2.348e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6915.00 ave 6915 max 6915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92350.0 ave 92350 max 92350 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184700.0 ave 184700 max 184700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184700 Ave neighs/atom = 174.90530 Neighbor list builds = 0 Dangerous builds = 0 1056 -4629.55083032652 eV 2.3089259756949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02