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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -53.845896 0.0000000) to (43.964990 53.845896 8.9126361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4203412 5.1633051 5.9417574 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -53.845896 0.0000000) to (43.964990 53.845896 8.9126361) create_atoms CPU = 0.002 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4203412 5.1633051 5.9417574 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.845896 0.0000000) to (43.964990 53.845896 8.9126361) create_atoms CPU = 0.002 seconds 1756 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3502 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 13.39 | 13.39 | 13.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9206.0164 0 -9206.0164 161609.91 59 0 -11881.875 0 -11881.875 3333.4321 Loop time of 5.3912 on 1 procs for 59 steps with 3502 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 = -9206.01635380549 -11881.8642649438 -11881.8750636985 Force two-norm initial, final = 3182.3351 0.28409042 Force max component initial, final = 441.01410 0.012757706 Final line search alpha, max atom move = 1.0000000 0.012757706 Iterations, force evaluations = 59 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2329 | 5.2329 | 5.2329 | 0.0 | 97.06 Neigh | 0.11347 | 0.11347 | 0.11347 | 0.0 | 2.10 Comm | 0.023226 | 0.023226 | 0.023226 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02163 | | | 0.40 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15213.0 ave 15213 max 15213 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: 1.11281e+06 ave 1.11281e+06 max 1.11281e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112810 Ave neighs/atom = 317.76413 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.39 | 13.39 | 13.39 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -11881.875 0 -11881.875 3333.4321 42198.378 64 0 -11882.201 0 -11882.201 71.543144 42294.597 Loop time of 0.423917 on 1 procs for 5 steps with 3502 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11881.8750636984 -11882.2007486969 -11882.2014290717 Force two-norm initial, final = 192.00737 5.2123809 Force max component initial, final = 179.71564 4.9819079 Final line search alpha, max atom move = 9.4371608e-05 0.00047015066 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41739 | 0.41739 | 0.41739 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009994 | 0.0009994 | 0.0009994 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005526 | | | 1.30 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15236.0 ave 15236 max 15236 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: 1.11319e+06 ave 1.11319e+06 max 1.11319e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1113186 Ave neighs/atom = 317.87150 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.90 | 12.90 | 12.90 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11882.201 0 -11882.201 71.543144 Loop time of 2.277e-06 on 1 procs for 0 steps with 3502 atoms 175.7% 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 | | 2.277e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15250.0 ave 15250 max 15250 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: 1.11265e+06 ave 1.11265e+06 max 1.11265e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112654 Ave neighs/atom = 317.71959 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.90 | 12.90 | 12.90 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 -11882.201 -11882.201 43.940583 108.11789 8.9026955 71.543144 71.543144 -24.394564 50.513079 188.51092 2.1841271 1584.5143 Loop time of 2.589e-06 on 1 procs for 0 steps with 3502 atoms 270.4% 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 | | 2.589e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15250.0 ave 15250 max 15250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 556327.0 ave 556327 max 556327 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.11265e+06 ave 1.11265e+06 max 1.11265e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1112654 Ave neighs/atom = 317.71959 Neighbor list builds = 0 Dangerous builds = 0 3502 -11882.2014290717 eV 2.18412707434983 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06