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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -69.206433 0.0000000) to (34.603216 69.206433 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2141833 5.2141833 4.0500001 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -69.206433 0.0000000) to (34.603216 69.206433 4.0500001) create_atoms CPU = 0.002 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2141833 5.2141833 4.0500001 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.206433 0.0000000) to (34.603216 69.206433 4.0500001) create_atoms CPU = 0.002 seconds 586 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 33 1 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1168 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_678952612413_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3892.4448 0 -3892.4448 3069.9716 25 0 -3915.3762 0 -3915.3762 3231.5692 Loop time of 0.999355 on 1 procs for 25 steps with 1168 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 = -3892.44478342051 -3915.37400897803 -3915.37623042752 Force two-norm initial, final = 18.149073 0.10564322 Force max component initial, final = 4.0985448 0.017298786 Final line search alpha, max atom move = 1.0000000 0.017298786 Iterations, force evaluations = 25 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98432 | 0.98432 | 0.98432 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083619 | 0.0083619 | 0.0083619 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006673 | | | 0.67 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8612.00 ave 8612 max 8612 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: 164544.0 ave 164544 max 164544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164544 Ave neighs/atom = 140.87671 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3915.3762 0 -3915.3762 3231.5692 19397.599 32 0 -3915.5912 0 -3915.5912 96.325212 19474.272 Loop time of 0.209436 on 1 procs for 7 steps with 1168 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 = -3915.37623042752 -3915.58989804543 -3915.59120018666 Force two-norm initial, final = 80.424093 2.0712458 Force max component initial, final = 74.486097 1.3832162 Final line search alpha, max atom move = 0.00032658658 0.00045173985 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20243 | 0.20243 | 0.20243 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015801 | 0.0015801 | 0.0015801 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005423 | | | 2.59 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8612.00 ave 8612 max 8612 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: 164628.0 ave 164628 max 164628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164628 Ave neighs/atom = 140.94863 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3915.5912 0 -3915.5912 96.325212 Loop time of 6.445e-06 on 1 procs for 0 steps with 1168 atoms 0.0% 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 | | 6.445e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8597.00 ave 8597 max 8597 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: 164344.0 ave 164344 max 164344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164344 Ave neighs/atom = 140.70548 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.208 | 5.208 | 5.208 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 -3915.5912 -3915.5912 34.568927 139.30199 4.044064 96.325212 96.325212 100.83496 114.53021 73.610472 2.5623922 612.23128 Loop time of 6.225e-06 on 1 procs for 0 steps with 1168 atoms 273.1% 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 | | 6.225e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8597.00 ave 8597 max 8597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82172.0 ave 82172 max 82172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164344.0 ave 164344 max 164344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164344 Ave neighs/atom = 140.70548 Neighbor list builds = 0 Dangerous builds = 0 1168 -3915.59120018666 eV 2.5623921686557 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01