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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -38.157772 0.0000000) to (31.155690 38.157772 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4508129 4.4128035 5.1393560 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -38.157772 0.0000000) to (31.155690 38.157772 7.7090341) create_atoms CPU = 0.003 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4508129 4.4128035 5.1393560 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -38.157772 0.0000000) to (31.155690 38.157772 7.7090341) create_atoms CPU = 0.002 seconds 590 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 25 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1178 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7583.4552 0 -7583.4552 90713.849 60 0 -7965.2449 0 -7965.2449 17168.928 Loop time of 1.41904 on 1 procs for 60 steps with 1178 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7583.45516500516 -7965.23732491864 -7965.24485311209 Force two-norm initial, final = 461.23668 0.35085137 Force max component initial, final = 148.80780 0.082898289 Final line search alpha, max atom move = 0.48344944 0.040077131 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3912 | 1.3912 | 1.3912 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010894 | 0.010894 | 0.010894 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01699 | | | 1.20 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3615.00 ave 3615 max 3615 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: 69080.0 ave 69080 max 69080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69080 Ave neighs/atom = 58.641766 Neighbor list builds = 0 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -7965.2449 0 -7965.2449 17168.928 18329.488 70 0 -7967.1819 0 -7967.1819 -69.834497 18432.369 Loop time of 0.154716 on 1 procs for 10 steps with 1178 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 = -7965.24485311208 -7967.17939230364 -7967.18189345091 Force two-norm initial, final = 465.48891 2.2059198 Force max component initial, final = 453.99944 1.1897898 Final line search alpha, max atom move = 9.4416361e-05 0.00011233562 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14762 | 0.14762 | 0.14762 | 0.0 | 95.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010499 | 0.0010499 | 0.0010499 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006044 | | | 3.91 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 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: 69128.0 ave 69128 max 69128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69128 Ave neighs/atom = 58.682513 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.680 | 4.680 | 4.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7967.1819 0 -7967.1819 -69.834497 Loop time of 6.496e-06 on 1 procs for 0 steps with 1178 atoms 184.7% 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 | | 6.496e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 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: 68908.0 ave 68908 max 68908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68908 Ave neighs/atom = 58.495756 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.680 | 4.680 | 4.680 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 -7967.1819 -7967.1819 31.084202 77.027929 7.6982712 -69.834497 -69.834497 -21.744517 -84.484575 -103.2744 2.3632201 994.17354 Loop time of 7.076e-06 on 1 procs for 0 steps with 1178 atoms 268.5% 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 | | 7.076e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3602.00 ave 3602 max 3602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34454.0 ave 34454 max 34454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68908.0 ave 68908 max 68908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68908 Ave neighs/atom = 58.495756 Neighbor list builds = 0 Dangerous builds = 0 1178 -7967.18189345091 eV 2.36322014203308 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42