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 -72.475108 0.0000000) to (41.843523 72.475108 6.2608958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6207718 5.7691629 6.2608958 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.475108 0.0000000) to (41.843523 72.475108 6.2608958) create_atoms CPU = 0.012 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6207718 5.7691629 6.2608958 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.475108 0.0000000) to (41.843523 72.475108 6.2608958) create_atoms CPU = 0.015 seconds 1610 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 = 16 53 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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 = 16 53 3 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) = 5.330 | 5.330 | 5.330 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10864.478 0 -10864.478 36341.779 50 0 -11385.064 0 -11385.064 4564.7959 Loop time of 2.60077 on 1 procs for 50 steps with 3218 atoms 74.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10864.4776193873 -11385.0621721137 -11385.0641670043 Force two-norm initial, final = 598.48108 1.5528013 Force max component initial, final = 166.33898 0.23045174 Final line search alpha, max atom move = 0.00083063463 0.00019142120 Iterations, force evaluations = 50 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4811 | 2.4811 | 2.4811 | 0.0 | 95.40 Neigh | 0.063447 | 0.063447 | 0.063447 | 0.0 | 2.44 Comm | 0.024673 | 0.024673 | 0.024673 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03159 | | | 1.21 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8465.00 ave 8465 max 8465 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: 174992.0 ave 174992 max 174992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174992 Ave neighs/atom = 54.379117 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 16 53 3 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.330 | 5.330 | 5.330 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -11385.064 0 -11385.064 4564.7959 37973.759 51 0 -11385.066 0 -11385.066 4542.8482 37974.355 Loop time of 0.233588 on 1 procs for 1 steps with 3218 atoms 74.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11385.0641670043 -11385.0641670043 -11385.0661052787 Force two-norm initial, final = 200.38490 199.50509 Force max component initial, final = 161.49174 160.89263 Final line search alpha, max atom move = 4.8377087e-08 7.7835165e-06 Iterations, force evaluations = 1 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22358 | 0.22358 | 0.22358 | 0.0 | 95.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020414 | 0.0020414 | 0.0020414 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007964 | | | 3.41 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476.00 ave 8476 max 8476 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: 175372.0 ave 175372 max 175372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175372 Ave neighs/atom = 54.497203 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 = 16 53 3 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) = 5.468 | 5.468 | 5.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11385.066 0 -11385.066 4542.8482 Loop time of 6.475e-06 on 1 procs for 0 steps with 3218 atoms 169.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476.00 ave 8476 max 8476 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: 175372.0 ave 175372 max 175372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175372 Ave neighs/atom = 54.497203 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 = 16 53 3 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) = 5.468 | 5.468 | 5.468 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 -11385.066 -11385.066 41.843728 144.95135 6.2609145 4542.8482 4542.8482 4248.5745 6788.2758 2591.6943 2.2852365 1294.1656 Loop time of 6.805e-06 on 1 procs for 0 steps with 3218 atoms 205.7% 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 | | 6.805e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476.00 ave 8476 max 8476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87686.0 ave 87686 max 87686 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175372.0 ave 175372 max 175372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175372 Ave neighs/atom = 54.497203 Neighbor list builds = 0 Dangerous builds = 0 3218 -11385.0661052787 eV 2.28523650292433 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03