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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -58.988734 0.0000000) to (29.492538 58.988734 3.6580991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0835822 4.0835822 3.6580991 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.988734 0.0000000) to (29.492538 58.988734 3.6580991) create_atoms CPU = 0.001 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0835822 4.0835822 3.6580991 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.988734 0.0000000) to (29.492538 58.988734 3.6580991) create_atoms CPU = 0.000 seconds 522 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1028 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3975.1765 0 -3975.1765 -2249.5327 58 0 -3995.8502 0 -3995.8502 -7453.3372 Loop time of 0.668031 on 1 procs for 58 steps with 1028 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 = -3975.1765463425 -3995.84630675752 -3995.85015159459 Force two-norm initial, final = 20.980450 0.18001618 Force max component initial, final = 7.2970879 0.031256402 Final line search alpha, max atom move = 1.0000000 0.031256402 Iterations, force evaluations = 58 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65822 | 0.65822 | 0.65822 | 0.0 | 98.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0053125 | 0.0053125 | 0.0053125 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004502 | | | 0.67 Nlocal: 1028.00 ave 1028 max 1028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7567.00 ave 7567 max 7567 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: 135964.0 ave 135964 max 135964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135964 Ave neighs/atom = 132.26070 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3995.8502 0 -3995.8502 -7453.3372 12728.191 298 0 -4041.1794 0 -4041.1794 46669.794 11550.82 Loop time of 1.90858 on 1 procs for 240 steps with 1028 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3995.85015159459 -4041.17816751619 -4041.17942653815 Force two-norm initial, final = 95.695747 7.7145044 Force max component initial, final = 85.517449 5.7331614 Final line search alpha, max atom move = 0.00045003584 0.0025801281 Iterations, force evaluations = 240 257 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7811 | 1.7811 | 1.7811 | 0.0 | 93.32 Neigh | 0.042585 | 0.042585 | 0.042585 | 0.0 | 2.23 Comm | 0.014897 | 0.014897 | 0.014897 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06999 | | | 3.67 Nlocal: 1028.00 ave 1028 max 1028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8192.00 ave 8192 max 8192 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: 156852.0 ave 156852 max 156852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156852 Ave neighs/atom = 152.57977 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4041.1794 0 -4041.1794 46669.794 Loop time of 1.812e-06 on 1 procs for 0 steps with 1028 atoms 110.4% 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 | | 1.812e-06 | | |100.00 Nlocal: 1028.00 ave 1028 max 1028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8192.00 ave 8192 max 8192 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: 157184.0 ave 157184 max 157184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157184 Ave neighs/atom = 152.90272 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.161 | 5.161 | 5.161 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 -4041.1794 -4041.1794 24.445836 117.97747 4.0050585 46669.794 46669.794 -659.15028 141118.22 -449.68864 2.1672048 480.97475 Loop time of 1.582e-06 on 1 procs for 0 steps with 1028 atoms 189.6% 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 | | 1.582e-06 | | |100.00 Nlocal: 1028.00 ave 1028 max 1028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8192.00 ave 8192 max 8192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78592.0 ave 78592 max 78592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157184.0 ave 157184 max 157184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157184 Ave neighs/atom = 152.90272 Neighbor list builds = 0 Dangerous builds = 0 1028 -3895.79799715535 eV 2.16720484580876 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02