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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -45.196806 0.0000000) to (27.677278 45.196806 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4640772 4.3738845 4.6866905 Created 743 atoms using lattice units in orthogonal box = (0.0000000 -45.196806 0.0000000) to (27.677278 45.196806 7.0300358) create_atoms CPU = 0.004 seconds 743 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4640772 4.3738845 4.6866905 Created 749 atoms using lattice units in orthogonal box = (0.0000000 -45.196806 0.0000000) to (27.677278 45.196806 7.0300358) create_atoms CPU = 0.003 seconds 749 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1488 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5884.5582 0 -5884.5582 36651.747 70 0 -6339.3945 0 -6339.3945 9025.2858 Loop time of 1.37505 on 1 procs for 70 steps with 1488 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 = -5884.55823226066 -6339.39056657816 -6339.39448062974 Force two-norm initial, final = 363.20018 0.20041707 Force max component initial, final = 54.949934 0.026754545 Final line search alpha, max atom move = 1.0000000 0.026754545 Iterations, force evaluations = 70 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2993 | 1.2993 | 1.2993 | 0.0 | 94.49 Neigh | 0.039558 | 0.039558 | 0.039558 | 0.0 | 2.88 Comm | 0.015518 | 0.015518 | 0.015518 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02071 | | | 1.51 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5073.00 ave 5073 max 5073 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: 98512.0 ave 98512 max 98512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98512 Ave neighs/atom = 66.204301 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -6339.3945 0 -6339.3945 9025.2858 17588.089 79 0 -6340.2696 0 -6340.2696 -77.1426 17682.635 Loop time of 0.120659 on 1 procs for 9 steps with 1488 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 = -6339.39448062975 -6340.2683236278 -6340.26958444387 Force two-norm initial, final = 231.08313 1.5901385 Force max component initial, final = 225.24691 0.94484172 Final line search alpha, max atom move = 0.00016484502 0.00015575246 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1137 | 0.1137 | 0.1137 | 0.0 | 94.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012727 | 0.0012727 | 0.0012727 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00569 | | | 4.72 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5337.00 ave 5337 max 5337 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: 97272.0 ave 97272 max 97272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97272 Ave neighs/atom = 65.370968 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6340.2696 0 -6340.2696 -77.1426 Loop time of 6.094e-06 on 1 procs for 0 steps with 1488 atoms 196.9% 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 | | 6.094e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5362.00 ave 5362 max 5362 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: 97104.0 ave 97104 max 97104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97104 Ave neighs/atom = 65.258065 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.813 | 4.813 | 4.813 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 -6340.2696 -6340.2696 27.625914 91.145431 7.0225597 -77.1426 -77.1426 -85.450713 -69.15247 -76.824618 2.295407 1039.983 Loop time of 7.577e-06 on 1 procs for 0 steps with 1488 atoms 250.8% 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 | | 7.577e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5362.00 ave 5362 max 5362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48552.0 ave 48552 max 48552 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97104.0 ave 97104 max 97104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97104 Ave neighs/atom = 65.258065 Neighbor list builds = 0 Dangerous builds = 0 1488 -6340.26943564387 eV 2.29540701146506 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02