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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5394348 4.4928753 4.9600000 Created 311 atoms using lattice units in orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) create_atoms CPU = 0.002 seconds 311 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5394348 4.4928753 4.9600000 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) create_atoms CPU = 0.002 seconds 317 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 ghost atom cutoff = 6 binsize = 3, bins = 9 20 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 626 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_162036141261_001#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 ghost atom cutoff = 6 binsize = 3, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2438.5759 0 -2438.5759 80386.396 65 0 -2667.4202 0 -2667.4202 15080.412 Loop time of 5.07099 on 1 procs for 65 steps with 626 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 = -2438.57585822444 -2667.41758192181 -2667.42022126735 Force two-norm initial, final = 481.59676 0.17949921 Force max component initial, final = 168.50485 0.044832432 Final line search alpha, max atom move = 1.0000000 0.044832432 Iterations, force evaluations = 65 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0349 | 5.0349 | 5.0349 | 0.0 | 99.29 Neigh | 0.016197 | 0.016197 | 0.016197 | 0.0 | 0.32 Comm | 0.0095453 | 0.0095453 | 0.0095453 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01032 | | | 0.20 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3078.00 ave 3078 max 3078 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: 40750.0 ave 40750 max 40750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40750 Ave neighs/atom = 65.095847 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 ghost atom cutoff = 6 binsize = 3, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -2667.4202 0 -2667.4202 15080.412 7326.8574 73 0 -2667.8314 0 -2667.8314 -8.0034392 7390.2737 Loop time of 0.488781 on 1 procs for 8 steps with 626 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 = -2667.42022126735 -2667.83120461475 -2667.83139606633 Force two-norm initial, final = 127.67831 0.36140306 Force max component initial, final = 104.10504 0.11224244 Final line search alpha, max atom move = 0.00041244968 4.6294357e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4849 | 0.4849 | 0.4849 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081387 | 0.00081387 | 0.00081387 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003066 | | | 0.63 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3077.00 ave 3077 max 3077 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: 40734.0 ave 40734 max 40734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40734 Ave neighs/atom = 65.070288 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 ghost atom cutoff = 6 binsize = 3, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2667.8314 0 -2667.8314 -8.0034392 Loop time of 6.314e-06 on 1 procs for 0 steps with 626 atoms 174.2% 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 | | 6.314e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3077.00 ave 3077 max 3077 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: 40620.0 ave 40620 max 40620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40620 Ave neighs/atom = 64.888179 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 ghost atom cutoff = 6 binsize = 3, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.631 | 4.631 | 4.631 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 -2667.8314 -2667.8314 25.282977 58.809151 4.970355 -8.0034392 -8.0034392 -24.32578 -20.613725 20.929187 2.3036931 650.72094 Loop time of 6.505e-06 on 1 procs for 0 steps with 626 atoms 261.3% 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 | | 6.505e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3077.00 ave 3077 max 3077 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20310.0 ave 20310 max 20310 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40620.0 ave 40620 max 40620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40620 Ave neighs/atom = 64.888179 Neighbor list builds = 0 Dangerous builds = 0 626 -2667.83139606633 eV 2.30369311855481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06