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 -39.809281 0.0000000) to (9.9523202 39.809281 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9809281 3.9809281 3.1472000 Created 80 atoms using lattice units in orthogonal box = (0.0000000 -39.809281 0.0000000) to (9.9523202 39.809281 3.1472000) create_atoms CPU = 0.001 seconds 80 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9809281 3.9809281 3.1472000 Created 82 atoms using lattice units in orthogonal box = (0.0000000 -39.809281 0.0000000) to (9.9523202 39.809281 3.1472000) create_atoms CPU = 0.001 seconds 82 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 = 4 26 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 160 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 = 4 26 2 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) = 4.378 | 4.378 | 4.378 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1073.4059 0 -1073.4059 37698.903 32 0 -1084.0448 0 -1084.0448 12076.769 Loop time of 0.121334 on 1 procs for 32 steps with 160 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 = -1073.40588804056 -1084.04421948155 -1084.04476320977 Force two-norm initial, final = 50.294142 0.097590363 Force max component initial, final = 18.503365 0.022208445 Final line search alpha, max atom move = 1.0000000 0.022208445 Iterations, force evaluations = 32 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11736 | 0.11736 | 0.11736 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024263 | 0.0024263 | 0.0024263 | 0.0 | 2.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001544 | | | 1.27 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1890.00 ave 1890 max 1890 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: 9352.00 ave 9352 max 9352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9352 Ave neighs/atom = 58.450000 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 = 4 26 2 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.378 | 4.378 | 4.378 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1084.0448 0 -1084.0448 12076.769 2493.8079 41 0 -1084.2339 0 -1084.2339 -38.714112 2504.3972 Loop time of 0.0229826 on 1 procs for 9 steps with 160 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 = -1084.04476320977 -1084.23376230455 -1084.23386430231 Force two-norm initial, final = 50.263531 0.45988779 Force max component initial, final = 50.044556 0.21133752 Final line search alpha, max atom move = 0.0016649859 0.00035187398 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021105 | 0.021105 | 0.021105 | 0.0 | 91.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043721 | 0.00043721 | 0.00043721 | 0.0 | 1.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00144 | | | 6.27 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1890.00 ave 1890 max 1890 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: 9312.00 ave 9312 max 9312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9312 Ave neighs/atom = 58.200000 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 = 4 26 2 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1084.2339 0 -1084.2339 -38.714112 Loop time of 6.866e-06 on 1 procs for 0 steps with 160 atoms 116.5% 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 | | 6.866e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1890.00 ave 1890 max 1890 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: 9296.00 ave 9296 max 9296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9296 Ave neighs/atom = 58.100000 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 = 4 26 2 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) = 4.516 | 4.516 | 4.516 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 -1084.2339 -1084.2339 9.932312 80.269736 3.1412393 -38.714112 -38.714112 49.266709 -136.30797 -29.101071 2.5042707 72.444251 Loop time of 6.705e-06 on 1 procs for 0 steps with 160 atoms 283.4% 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 | | 6.705e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1890.00 ave 1890 max 1890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4648.00 ave 4648 max 4648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9296.00 ave 9296 max 9296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9296 Ave neighs/atom = 58.100000 Neighbor list builds = 0 Dangerous builds = 0 160 -1084.23386430231 eV 2.50427070791579 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42