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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -36.147299 0.0000000) to (5.1120000 36.147299 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1120000 3.6147299 5.1120000 Created 80 atoms using lattice units in orthogonal box = (0.0000000 -36.147299 0.0000000) to (5.1120000 36.147299 5.1120000) create_atoms CPU = 0.001 seconds 80 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1120000 3.6147299 5.1120000 Created 84 atoms using lattice units in orthogonal box = (0.0000000 -36.147299 0.0000000) to (5.1120000 36.147299 5.1120000) create_atoms CPU = 0.000 seconds 84 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 2 27 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 164 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 2 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -485.40361 0 -485.40361 167219.6 34 0 -584.36561 0 -584.36561 30699.364 Loop time of 0.908703 on 1 procs for 34 steps with 164 atoms 28.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -485.403607692561 -584.365613558983 -584.365613558983 Force two-norm initial, final = 153.22189 0.32514438 Force max component initial, final = 38.084176 0.051351446 Final line search alpha, max atom move = 1.1920929e-07 6.1215694e-09 Iterations, force evaluations = 34 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89852 | 0.89852 | 0.89852 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0060611 | 0.0060611 | 0.0060611 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004125 | | | 0.45 Nlocal: 164.000 ave 164 max 164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1708.00 ave 1708 max 1708 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: 9192.00 ave 9192 max 9192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9192 Ave neighs/atom = 56.048780 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 2 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -584.36561 0 -584.36561 30699.364 1889.2417 38 0 -584.5394 0 -584.5394 22600.554 1899.4186 Loop time of 0.122757 on 1 procs for 4 steps with 164 atoms 29.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -584.365613558983 -584.539260766547 -584.539403444912 Force two-norm initial, final = 63.397300 47.192496 Force max component initial, final = 40.102061 30.492917 Final line search alpha, max atom move = 6.4032594e-08 1.9525406e-06 Iterations, force evaluations = 4 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11963 | 0.11963 | 0.11963 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073884 | 0.00073884 | 0.00073884 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002387 | | | 1.94 Nlocal: 164.000 ave 164 max 164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1732.00 ave 1732 max 1732 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: 9072.00 ave 9072 max 9072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9072 Ave neighs/atom = 55.317073 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 2 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -584.5394 0 -584.5394 22600.554 Loop time of 6.224e-06 on 1 procs for 0 steps with 164 atoms 192.8% 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 | | 6.224e-06 | | |100.00 Nlocal: 164.000 ave 164 max 164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1725.00 ave 1725 max 1725 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: 9024.00 ave 9024 max 9024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9024 Ave neighs/atom = 55.024390 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 2 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.544 | 4.544 | 4.544 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 -584.5394 -584.5394 5.122193 72.39446 5.122234 22600.554 22600.554 25657.27 16371.853 25772.539 2.4780657 0.12859888 Loop time of 6.014e-06 on 1 procs for 0 steps with 164 atoms 83.1% 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 | | 6.014e-06 | | |100.00 Nlocal: 164.000 ave 164 max 164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4512.00 ave 4512 max 4512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9024.00 ave 9024 max 9024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9024 Ave neighs/atom = 55.024390 Neighbor list builds = 0 Dangerous builds = 0 164 -584.539403444912 eV 2.47806573325855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01