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 -37.238172 0.0000000) to (45.607261 37.238172 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2122583 4.7877650 5.1393560 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -37.238172 0.0000000) to (45.607261 37.238172 7.7090341) create_atoms CPU = 0.005 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2122583 4.7877650 5.1393560 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -37.238172 0.0000000) to (45.607261 37.238172 7.7090341) create_atoms CPU = 0.004 seconds 841 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 = 15 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1669 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 = 15 24 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9878.7026 0 -9878.7026 95086.119 176 0 -11290.348 0 -11290.348 -8286.2829 Loop time of 5.35638 on 1 procs for 176 steps with 1669 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9878.70255845005 -11290.3381823103 -11290.3484125183 Force two-norm initial, final = 1146.6938 0.46709775 Force max component initial, final = 215.61702 0.087504124 Final line search alpha, max atom move = 0.58700228 0.051365121 Iterations, force evaluations = 176 343 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2192 | 5.2192 | 5.2192 | 0.0 | 97.44 Neigh | 0.039861 | 0.039861 | 0.039861 | 0.0 | 0.74 Comm | 0.037981 | 0.037981 | 0.037981 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05931 | | | 1.11 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4928.00 ave 4928 max 4928 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: 97768.0 ave 97768 max 97768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97768 Ave neighs/atom = 58.578790 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 15 24 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 : 176 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press Volume 176 0 -11290.348 0 -11290.348 -8286.2829 26184.983 179 0 -11290.578 0 -11290.578 -8.2786613 26111.527 Loop time of 0.0950798 on 1 procs for 3 steps with 1669 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11290.3484125183 -11290.5706749835 -11290.5775913614 Force two-norm initial, final = 242.04716 0.68616937 Force max component initial, final = 174.08565 0.19624742 Final line search alpha, max atom move = 3.2049823e-05 6.2896951e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091636 | 0.091636 | 0.091636 | 0.0 | 96.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061511 | 0.00061511 | 0.00061511 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002829 | | | 2.98 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4916.00 ave 4916 max 4916 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: 97798.0 ave 97798 max 97798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97798 Ave neighs/atom = 58.596765 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 = 15 24 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) = 4.763 | 4.763 | 4.763 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11290.578 0 -11290.578 -8.2786613 Loop time of 6.224e-06 on 1 procs for 0 steps with 1669 atoms 176.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4916.00 ave 4916 max 4916 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: 97838.0 ave 97838 max 97838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97838 Ave neighs/atom = 58.620731 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 = 15 24 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) = 4.763 | 4.763 | 4.763 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 -11290.578 -11290.578 45.558508 74.477893 7.6954743 -8.2786613 -8.2786613 -8.0464235 -4.7692003 -12.02036 2.4171852 2031.2464 Loop time of 7.126e-06 on 1 procs for 0 steps with 1669 atoms 252.6% 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 | | 7.126e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4916.00 ave 4916 max 4916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48919.0 ave 48919 max 48919 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97838.0 ave 97838 max 97838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97838 Ave neighs/atom = 58.620731 Neighbor list builds = 0 Dangerous builds = 0 1669 -11290.5775913614 eV 2.4171852066829 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42