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 -33.008112 0.0000000) to (40.426516 33.008112 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1451929 4.8011799 5.1393560 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -33.008112 0.0000000) to (40.426516 33.008112 7.7090341) create_atoms CPU = 0.004 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1451929 4.8011799 5.1393560 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -33.008112 0.0000000) to (40.426516 33.008112 7.7090341) create_atoms CPU = 0.003 seconds 662 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 = 13 22 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 12 atoms, new total = 1306 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 = 13 22 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7955.1181 0 -7955.1181 89228.478 252 0 -8825.3 0 -8825.3 -15753.74 Loop time of 5.99943 on 1 procs for 252 steps with 1306 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 = -7955.11814520584 -8825.29302871719 -8825.29996757626 Force two-norm initial, final = 846.84654 0.40893448 Force max component initial, final = 161.06051 0.079905045 Final line search alpha, max atom move = 0.84085774 0.067188776 Iterations, force evaluations = 252 488 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8412 | 5.8412 | 5.8412 | 0.0 | 97.36 Neigh | 0.046218 | 0.046218 | 0.046218 | 0.0 | 0.77 Comm | 0.045117 | 0.045117 | 0.045117 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06688 | | | 1.11 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4077.00 ave 4077 max 4077 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: 76470.0 ave 76470 max 76470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76470 Ave neighs/atom = 58.552833 Neighbor list builds = 3 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 = 13 22 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 : 252 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -8825.3 0 -8825.3 -15753.74 20573.916 257 0 -8825.903 0 -8825.903 10.913642 20463.431 Loop time of 0.112207 on 1 procs for 5 steps with 1306 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 = -8825.29996757626 -8825.90295772599 -8825.90300750533 Force two-norm initial, final = 356.41706 1.4358350 Force max component initial, final = 247.92485 1.0075886 Final line search alpha, max atom move = 0.0014908910 0.0015022048 Iterations, force evaluations = 5 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10782 | 0.10782 | 0.10782 | 0.0 | 96.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075888 | 0.00075888 | 0.00075888 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003627 | | | 3.23 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4071.00 ave 4071 max 4071 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: 76338.0 ave 76338 max 76338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76338 Ave neighs/atom = 58.451761 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 = 13 22 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8825.903 0 -8825.903 10.913642 Loop time of 6.285e-06 on 1 procs for 0 steps with 1306 atoms 175.0% 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 | | 6.285e-06 | | |100.00 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4086.00 ave 4086 max 4086 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: 76460.0 ave 76460 max 76460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76460 Ave neighs/atom = 58.545176 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 = 13 22 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) = 4.729 | 4.729 | 4.729 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 -8825.903 -8825.903 40.407576 65.814744 7.6947137 10.913642 10.913642 -29.248192 -16.753101 78.74222 2.3923307 1675.7724 Loop time of 7.027e-06 on 1 procs for 0 steps with 1306 atoms 270.4% 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 | | 7.027e-06 | | |100.00 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4086.00 ave 4086 max 4086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38230.0 ave 38230 max 38230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76460.0 ave 76460 max 76460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76460 Ave neighs/atom = 58.545176 Neighbor list builds = 0 Dangerous builds = 0 1306 -8825.90300750533 eV 2.39233066215861 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42