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 -35.606503 0.0000000) to (15.418068 35.606503 5.4511103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1393560 4.4508129 5.4511103 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -35.606503 0.0000000) to (15.418068 35.606503 5.4511103) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1393560 4.4508129 5.4511103 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.606503 0.0000000) to (15.418068 35.606503 5.4511103) create_atoms CPU = 0.000 seconds 204 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 = 5 23 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 0 atoms, new total = 396 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 = 5 23 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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1080.9201 0 -1080.9201 502535.08 57 0 -2684.6762 0 -2684.6762 105336.78 Loop time of 0.190288 on 1 procs for 57 steps with 396 atoms 94.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1080.92014880295 -2684.67380847628 -2684.67618666709 Force two-norm initial, final = 990.01830 0.21479719 Force max component initial, final = 297.17859 0.019877712 Final line search alpha, max atom move = 1.0000000 0.019877712 Iterations, force evaluations = 57 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18445 | 0.18445 | 0.18445 | 0.0 | 96.93 Neigh | 0.0019579 | 0.0019579 | 0.0019579 | 0.0 | 1.03 Comm | 0.0018942 | 0.0018942 | 0.0018942 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001981 | | | 1.04 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2252.00 ave 2252 max 2252 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: 24128.0 ave 24128 max 24128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24128 Ave neighs/atom = 60.929293 Neighbor list builds = 1 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 = 5 23 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -2684.6762 0 -2684.6762 105336.78 5985.1391 94 0 -2694.7789 0 -2694.7789 -119.63302 6180.9363 Loop time of 0.0838804 on 1 procs for 37 steps with 396 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 = -2684.67618666709 -2694.77814622061 -2694.77888147209 Force two-norm initial, final = 741.55649 2.1897167 Force max component initial, final = 631.95851 1.2557687 Final line search alpha, max atom move = 0.00022524268 0.00028285271 Iterations, force evaluations = 37 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075025 | 0.075025 | 0.075025 | 0.0 | 89.44 Neigh | 0.0038818 | 0.0038818 | 0.0038818 | 0.0 | 4.63 Comm | 0.00087654 | 0.00087654 | 0.00087654 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004097 | | | 4.88 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2208.00 ave 2208 max 2208 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: 23120.0 ave 23120 max 23120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23120 Ave neighs/atom = 58.383838 Neighbor list builds = 2 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 = 5 24 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2694.7789 0 -2694.7789 -119.63302 Loop time of 1.356e-06 on 1 procs for 0 steps with 396 atoms 221.2% 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 | | 1.356e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2208.00 ave 2208 max 2208 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: 23144.0 ave 23144 max 23144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23144 Ave neighs/atom = 58.444444 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 = 5 24 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) = 4.579 | 4.579 | 4.579 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 -2694.7789 -2694.7789 15.420656 73.578783 5.4475199 -119.63302 -119.63302 -325.5657 13.846393 -47.179769 2.6336918 144.86042 Loop time of 1.998e-06 on 1 procs for 0 steps with 396 atoms 150.2% 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 | | 1.998e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2208.00 ave 2208 max 2208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11572.0 ave 11572 max 11572 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23144.0 ave 23144 max 23144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23144 Ave neighs/atom = 58.444444 Neighbor list builds = 0 Dangerous builds = 0 396 -2694.77888147209 eV 2.63369175516885 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