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 -36.431474 0.0000000) to (25.760942 36.431474 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9983917 5.4375334 4.4508129 Created 267 atoms using lattice units in orthogonal box = (0.0000000 -36.431474 0.0000000) to (25.760942 36.431474 4.4508129) create_atoms CPU = 0.001 seconds 267 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9983917 5.4375334 4.4508129 Created 269 atoms using lattice units in orthogonal box = (0.0000000 -36.431474 0.0000000) to (25.760942 36.431474 4.4508129) create_atoms CPU = 0.001 seconds 269 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 = 9 24 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 = 536 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 = 9 24 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3180.4584 0 -3180.4584 136094.73 74 0 -3625.7658 0 -3625.7658 10209.043 Loop time of 0.413745 on 1 procs for 74 steps with 536 atoms 75.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3180.4584039922 -3625.7625125172 -3625.76576209747 Force two-norm initial, final = 591.50415 0.23044122 Force max component initial, final = 164.45581 0.037640035 Final line search alpha, max atom move = 1.0000000 0.037640035 Iterations, force evaluations = 74 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40252 | 0.40252 | 0.40252 | 0.0 | 97.29 Neigh | 0.0053509 | 0.0053509 | 0.0053509 | 0.0 | 1.29 Comm | 0.0029745 | 0.0029745 | 0.0029745 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002901 | | | 0.70 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2706.00 ave 2706 max 2706 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: 31410.0 ave 31410 max 31410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31410 Ave neighs/atom = 58.600746 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 = 9 24 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -3625.7658 0 -3625.7658 10209.043 8354.2566 80 0 -3626.079 0 -3626.079 -283.06513 8382.7687 Loop time of 0.0189136 on 1 procs for 6 steps with 536 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 = -3625.76576209747 -3626.07848412052 -3626.07896007462 Force two-norm initial, final = 122.27068 3.0452372 Force max component initial, final = 110.59390 2.4809465 Final line search alpha, max atom move = 0.00023493482 0.00058286073 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017954 | 0.017954 | 0.017954 | 0.0 | 94.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017558 | 0.00017558 | 0.00017558 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007837 | | | 4.14 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2718.00 ave 2718 max 2718 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: 31384.0 ave 31384 max 31384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31384 Ave neighs/atom = 58.552239 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 = 9 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3626.079 0 -3626.079 -283.06513 Loop time of 1.34e-06 on 1 procs for 0 steps with 536 atoms 149.3% 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 | | 1.34e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2718.00 ave 2718 max 2718 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: 31342.0 ave 31342 max 31342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31342 Ave neighs/atom = 58.473881 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 = 9 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) = 4.600 | 4.600 | 4.600 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 -3626.079 -3626.079 25.78838 73.234171 4.4386372 -283.06513 -283.06513 -297.51445 -78.801327 -472.87961 2.4480133 475.49188 Loop time of 1.399e-06 on 1 procs for 0 steps with 536 atoms 143.0% 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 | | 1.399e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2718.00 ave 2718 max 2718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15671.0 ave 15671 max 15671 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31342.0 ave 31342 max 31342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31342 Ave neighs/atom = 58.473881 Neighbor list builds = 0 Dangerous builds = 0 536 -3626.07896007462 eV 2.44801329887948 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