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 = 3.5222108 3.5222108 3.5222108 Created orthogonal box = (0.0000000 -62.214647 0.0000000) to (35.919643 62.214647 6.1006480) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5260989 5.5833657 6.1006480 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -62.214647 0.0000000) to (35.919643 62.214647 6.1006480) create_atoms CPU = 0.003 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5260989 5.5833657 6.1006480 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -62.214647 0.0000000) to (35.919643 62.214647 6.1006480) create_atoms CPU = 0.002 seconds 1252 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 38 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2500 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_468686727341_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 6.108 | 6.108 | 6.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14298.699 0 -14298.699 8633.4946 82 0 -14410.359 0 -14410.359 13599.4 Loop time of 208.836 on 1 procs for 82 steps with 2500 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14298.6990821032 -14410.3471290871 -14410.3594257548 Force two-norm initial, final = 40.133106 0.32117820 Force max component initial, final = 5.0700417 0.052839121 Final line search alpha, max atom move = 1.0000000 0.052839121 Iterations, force evaluations = 82 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 208.75 | 208.75 | 208.75 | 0.0 | 99.96 Neigh | 0.041139 | 0.041139 | 0.041139 | 0.0 | 0.02 Comm | 0.019365 | 0.019365 | 0.019365 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02287 | | | 0.01 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8822.00 ave 8822 max 8822 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: 312848.0 ave 312848 max 312848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312848 Ave neighs/atom = 125.13920 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.098 | 6.098 | 6.098 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -14410.359 0 -14410.359 13599.4 27266.577 91 0 -14412.078 0 -14412.078 -43.786965 27458.901 Loop time of 15.2888 on 1 procs for 9 steps with 2500 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 = -14410.3594257548 -14412.078166316 -14412.0783960886 Force two-norm initial, final = 486.67703 2.0760797 Force max component initial, final = 452.89427 1.7299379 Final line search alpha, max atom move = 0.00020719515 0.00035843475 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.262 | 15.262 | 15.262 | 0.0 | 99.83 Neigh | 0.019406 | 0.019406 | 0.019406 | 0.0 | 0.13 Comm | 0.0011252 | 0.0011252 | 0.0011252 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006198 | | | 0.04 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8810.00 ave 8810 max 8810 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: 303032.0 ave 303032 max 303032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303032 Ave neighs/atom = 121.21280 Neighbor list builds = 1 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 6.237 | 6.237 | 6.237 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14412.078 0 -14412.078 -43.786965 Loop time of 1.8e-06 on 1 procs for 0 steps with 2500 atoms 222.2% 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 | | 1.8e-06 | | |100.00 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8810.00 ave 8810 max 8810 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: 310432.0 ave 310432 max 310432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310432 Ave neighs/atom = 124.17280 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 6.237 | 6.237 | 6.237 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 -14412.078 -14412.078 35.920603 125.40708 6.0956141 -43.786965 -43.786965 -100.9414 -52.915492 22.495999 2.1946979 966.5764 Loop time of 2.444e-06 on 1 procs for 0 steps with 2500 atoms 204.6% 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 | | 2.444e-06 | | |100.00 Nlocal: 2500.00 ave 2500 max 2500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8810.00 ave 8810 max 8810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155216.0 ave 155216 max 155216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 310432.0 ave 310432 max 310432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310432 Ave neighs/atom = 124.17280 Neighbor list builds = 0 Dangerous builds = 0 2500 -7082.92072917605 eV 2.19469789317246 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:03:49