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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -40.901043 0.0000000) to (28.921405 40.901043 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5366909 3.6089155 4.0498067 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -40.901043 0.0000000) to (28.921405 40.901043 4.0498067) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5366909 3.6089155 4.0498067 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -40.901043 0.0000000) to (28.921405 40.901043 4.0498067) create_atoms CPU = 0.001 seconds 409 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 25 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 812 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_260546967793_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2972.4618 0 -2972.4618 86343.394 81 0 -3465.5988 0 -3465.5988 445.00728 Loop time of 12.4466 on 1 procs for 81 steps with 812 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 = -2972.46175694536 -3465.59624664534 -3465.59880836666 Force two-norm initial, final = 891.04937 0.14922552 Force max component initial, final = 294.62271 0.024072297 Final line search alpha, max atom move = 1.0000000 0.024072297 Iterations, force evaluations = 81 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.417 | 12.417 | 12.417 | 0.0 | 99.76 Neigh | 0.01272 | 0.01272 | 0.01272 | 0.0 | 0.10 Comm | 0.0089505 | 0.0089505 | 0.0089505 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008274 | | | 0.07 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4744.00 ave 4744 max 4744 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: 90640.0 ave 90640 max 90640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90640 Ave neighs/atom = 111.62562 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -3465.5988 0 -3465.5988 445.00728 9581.159 84 0 -3465.639 0 -3465.639 -593.34252 9586.9123 Loop time of 0.461026 on 1 procs for 3 steps with 812 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 = -3465.59880836665 -3465.6359519256 -3465.63900142042 Force two-norm initial, final = 23.786537 6.6764425 Force max component initial, final = 21.667045 4.6816166 Final line search alpha, max atom move = 0.00012987506 0.00060802526 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45976 | 0.45976 | 0.45976 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021011 | 0.00021011 | 0.00021011 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001051 | | | 0.23 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4740.00 ave 4740 max 4740 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: 90686.0 ave 90686 max 90686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90686 Ave neighs/atom = 111.68227 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3465.639 0 -3465.639 -593.34252 Loop time of 2.294e-06 on 1 procs for 0 steps with 812 atoms 174.4% 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 | | 2.294e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4740.00 ave 4740 max 4740 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: 90634.0 ave 90634 max 90634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90634 Ave neighs/atom = 111.61823 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.686 | 4.686 | 4.686 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 -3465.639 -3465.639 28.893297 82.027595 4.0450293 -593.34252 -593.34252 -756.61832 -241.93471 -781.47454 2.3135212 476.27289 Loop time of 2.385e-06 on 1 procs for 0 steps with 812 atoms 167.7% 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 | | 2.385e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4740.00 ave 4740 max 4740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45317.0 ave 45317 max 45317 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90634.0 ave 90634 max 90634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90634 Ave neighs/atom = 111.61823 Neighbor list builds = 0 Dangerous builds = 0 812 -3465.63900142042 eV 2.31352115110807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13