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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -50.125935 0.0000000) to (13.642551 50.125935 8.9311464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8468078 5.5695483 5.9540976 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -50.125935 0.0000000) to (13.642551 50.125935 8.9311464) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8468078 5.5695483 5.9540976 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -50.125935 0.0000000) to (13.642551 50.125935 8.9311464) create_atoms CPU = 0.001 seconds 507 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 24 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.495 | 5.495 | 5.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3290.9333 0 -3290.9333 78281.345 51 0 -3915.6984 0 -3915.6984 4532.3273 Loop time of 0.69357 on 1 procs for 51 steps with 1008 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3290.93333853264 -3915.69455874674 -3915.69843087952 Force two-norm initial, final = 875.97603 0.26606230 Force max component initial, final = 187.17650 0.040746244 Final line search alpha, max atom move = 1.0000000 0.040746244 Iterations, force evaluations = 51 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6565 | 0.6565 | 0.6565 | 0.0 | 94.66 Neigh | 0.026479 | 0.026479 | 0.026479 | 0.0 | 3.82 Comm | 0.0054643 | 0.0054643 | 0.0054643 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005125 | | | 0.74 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6839.00 ave 6839 max 6839 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: 224762.0 ave 224762 max 224762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224762 Ave neighs/atom = 222.97817 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.495 | 5.495 | 5.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -3915.6984 0 -3915.6984 4532.3273 12215.051 54 0 -3915.7809 0 -3915.7809 260.42901 12246.512 Loop time of 0.0401774 on 1 procs for 3 steps with 1008 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 = -3915.69843087951 -3915.77805213825 -3915.78087312251 Force two-norm initial, final = 70.172364 3.8119246 Force max component initial, final = 60.967471 3.1803299 Final line search alpha, max atom move = 0.00010318282 0.00032815541 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038583 | 0.038583 | 0.038583 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028786 | 0.00028786 | 0.00028786 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001307 | | | 3.25 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6857.00 ave 6857 max 6857 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: 224764.0 ave 224764 max 224764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224764 Ave neighs/atom = 222.98016 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.633 | 5.633 | 5.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3915.7809 0 -3915.7809 260.42901 Loop time of 1.866e-06 on 1 procs for 0 steps with 1008 atoms 160.8% 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 | | 1.866e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6857.00 ave 6857 max 6857 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: 224692.0 ave 224692 max 224692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224692 Ave neighs/atom = 222.90873 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.633 | 5.633 | 5.633 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 -3915.7809 -3915.7809 13.672696 100.33194 8.9272782 260.42901 260.42901 416.99291 244.91713 119.37701 2.3413183 382.74025 Loop time of 2.411e-06 on 1 procs for 0 steps with 1008 atoms 165.9% 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 | | 2.411e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6857.00 ave 6857 max 6857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112346.0 ave 112346 max 112346 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224692.0 ave 224692 max 224692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224692 Ave neighs/atom = 222.90873 Neighbor list builds = 0 Dangerous builds = 0 1008 -3915.78087312251 eV 2.34131834457333 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01