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 = 2.8599998 2.8599998 2.8599998 Created orthogonal box = (0.0000000 -45.039322 0.0000000) to (27.580839 45.039322 7.0055402) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4485225 4.3586441 4.6703601 Created 740 atoms using lattice units in orthogonal box = (0.0000000 -45.039322 0.0000000) to (27.580839 45.039322 7.0055402) create_atoms CPU = 0.004 seconds 740 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4485225 4.3586441 4.6703601 Created 746 atoms using lattice units in orthogonal box = (0.0000000 -45.039322 0.0000000) to (27.580839 45.039322 7.0055402) create_atoms CPU = 0.003 seconds 746 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 34 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1486 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_857282754307_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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2107.3023 0 -2107.3023 32235.418 70 0 -2257.8762 0 -2257.8762 7512.0504 Loop time of 0.779015 on 1 procs for 70 steps with 1486 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 = -2107.30232866657 -2257.87405925501 -2257.87617576664 Force two-norm initial, final = 189.36792 0.19269999 Force max component initial, final = 37.522061 0.027903374 Final line search alpha, max atom move = 1.0000000 0.027903374 Iterations, force evaluations = 70 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72852 | 0.72852 | 0.72852 | 0.0 | 93.52 Neigh | 0.015927 | 0.015927 | 0.015927 | 0.0 | 2.04 Comm | 0.014166 | 0.014166 | 0.014166 | 0.0 | 1.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02041 | | | 2.62 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4679.00 ave 4679 max 4679 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: 85796.0 ave 85796 max 85796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85796 Ave neighs/atom = 57.736205 Neighbor list builds = 1 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -2257.8762 0 -2257.8762 7512.0504 17404.877 79 0 -2258.6464 0 -2258.6464 -8.2453265 17503.424 Loop time of 0.068403 on 1 procs for 9 steps with 1486 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 = -2257.87617576664 -2258.64423943385 -2258.64641886516 Force two-norm initial, final = 195.30520 0.62643145 Force max component initial, final = 190.41168 0.13283928 Final line search alpha, max atom move = 0.00014780418 1.9634201e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061886 | 0.061886 | 0.061886 | 0.0 | 90.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011432 | 0.0011432 | 0.0011432 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005373 | | | 7.86 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4688.00 ave 4688 max 4688 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: 85752.0 ave 85752 max 85752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85752 Ave neighs/atom = 57.706595 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.769 | 4.769 | 4.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2258.6464 0 -2258.6464 -8.2453265 Loop time of 6.655e-06 on 1 procs for 0 steps with 1486 atoms 180.3% 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 | | 6.655e-06 | | |100.00 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4693.00 ave 4693 max 4693 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: 85728.0 ave 85728 max 85728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85728 Ave neighs/atom = 57.690444 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.769 | 4.769 | 4.769 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 -2258.6464 -2258.6464 27.519421 90.837059 7.0019768 -8.2453265 -8.2453265 -7.327303 -12.261824 -5.1468526 2.3161148 941.43996 Loop time of 6.966e-06 on 1 procs for 0 steps with 1486 atoms 229.7% 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 | | 6.966e-06 | | |100.00 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4693.00 ave 4693 max 4693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42864.0 ave 42864 max 42864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85728.0 ave 85728 max 85728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85728 Ave neighs/atom = 57.690444 Neighbor list builds = 0 Dangerous builds = 0 1486 -2258.64641886516 eV 2.31611483271096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01