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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -50.687419 0.0000000) to (25.343710 50.687419 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5091290 3.5091290 3.1435003 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -50.687419 0.0000000) to (25.343710 50.687419 3.1435003) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5091290 3.5091290 3.1435003 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.687419 0.0000000) to (25.343710 50.687419 3.1435003) create_atoms CPU = 0.000 seconds 261 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.938 | 4.938 | 4.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2792.6819 0 -2792.6819 191041.21 92 0 -3473.4175 0 -3473.4175 14730.317 Loop time of 1.1946 on 1 procs for 92 steps with 521 atoms 91.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2792.68190962873 -3473.41406017646 -3473.41752167552 Force two-norm initial, final = 1421.5720 0.32747504 Force max component initial, final = 576.25713 0.056051048 Final line search alpha, max atom move = 0.83252471 0.046663883 Iterations, force evaluations = 92 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1635 | 1.1635 | 1.1635 | 0.0 | 97.40 Neigh | 0.014538 | 0.014538 | 0.014538 | 0.0 | 1.22 Comm | 0.010681 | 0.010681 | 0.010681 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00587 | | | 0.49 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7291.00 ave 7291 max 7291 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: 143954.0 ave 143954 max 143954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143954 Ave neighs/atom = 276.30326 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -3473.4175 0 -3473.4175 14730.317 8076.3263 212 0 -3480.2124 0 -3480.2124 -494.80755 8112.6349 Loop time of 1.01476 on 1 procs for 120 steps with 521 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3473.41752167552 -3480.21090388043 -3480.21237624019 Force two-norm initial, final = 186.32234 6.4150657 Force max component initial, final = 135.75898 3.6495873 Final line search alpha, max atom move = 0.00021068048 0.00076889682 Iterations, force evaluations = 120 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94827 | 0.94827 | 0.94827 | 0.0 | 93.45 Neigh | 0.022028 | 0.022028 | 0.022028 | 0.0 | 2.17 Comm | 0.0089927 | 0.0089927 | 0.0089927 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03547 | | | 3.50 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8175.00 ave 8175 max 8175 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: 142120.0 ave 142120 max 142120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142120 Ave neighs/atom = 272.78311 Neighbor list builds = 3 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3480.2124 0 -3480.2124 -494.80755 Loop time of 1.846e-06 on 1 procs for 0 steps with 521 atoms 162.5% 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 | | 1.846e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8175.00 ave 8175 max 8175 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: 141952.0 ave 141952 max 141952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141952 Ave neighs/atom = 272.46065 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.078 | 5.078 | 5.078 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 -3480.2124 -3480.2124 26.992283 101.08067 2.973406 -494.80755 -494.80755 -369.54656 -718.67098 -396.2051 2.5793101 249.55163 Loop time of 1.779e-06 on 1 procs for 0 steps with 521 atoms 112.4% 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 | | 1.779e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8175.00 ave 8175 max 8175 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70976.0 ave 70976 max 70976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141952.0 ave 141952 max 141952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141952 Ave neighs/atom = 272.46065 Neighbor list builds = 0 Dangerous builds = 0 521 -3480.2123762402 eV 2.57931006293609 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02