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 -46.574306 0.0000000) to (38.027762 46.574306 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6883542 4.4660294 5.1393560 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -46.574306 0.0000000) to (38.027762 46.574306 7.7090341) create_atoms CPU = 0.004 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6883542 4.4660294 5.1393560 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.574306 0.0000000) to (38.027762 46.574306 7.7090341) create_atoms CPU = 0.003 seconds 878 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 30 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 0 atoms, new total = 1754 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 30 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11481.083 0 -11481.083 69913.611 64 0 -11881.051 0 -11881.051 12805.317 Loop time of 2.04334 on 1 procs for 64 steps with 1754 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 = -11481.083276698 -11881.0404228791 -11881.0510925792 Force two-norm initial, final = 452.01165 0.49236218 Force max component initial, final = 118.42843 0.066197383 Final line search alpha, max atom move = 0.88586377 0.058641863 Iterations, force evaluations = 64 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0077 | 2.0077 | 2.0077 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014412 | 0.014412 | 0.014412 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0212 | | | 1.04 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5291.00 ave 5291 max 5291 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: 102644.0 ave 102644 max 102644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102644 Ave neighs/atom = 58.519954 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 = 13 30 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -11881.051 0 -11881.051 12805.317 27307.197 71 0 -11882.463 0 -11882.463 -215.08701 27427.117 Loop time of 0.167495 on 1 procs for 7 steps with 1754 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 = -11881.0510925792 -11882.4512697305 -11882.4625051083 Force two-norm initial, final = 487.74791 6.6488001 Force max component initial, final = 469.88188 4.8393546 Final line search alpha, max atom move = 3.5031938e-05 0.00016953197 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16006 | 0.16006 | 0.16006 | 0.0 | 95.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011879 | 0.0011879 | 0.0011879 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006247 | | | 3.73 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5291.00 ave 5291 max 5291 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: 102464.0 ave 102464 max 102464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102464 Ave neighs/atom = 58.417332 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 31 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) = 5.196 | 5.196 | 5.196 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11882.463 0 -11882.463 -215.08701 Loop time of 9.111e-06 on 1 procs for 0 steps with 1754 atoms 153.7% 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 | | 9.111e-06 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5277.00 ave 5277 max 5277 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: 102356.0 ave 102356 max 102356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102356 Ave neighs/atom = 58.355758 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 31 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) = 5.196 | 5.196 | 5.196 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 -11882.463 -11882.463 37.989811 93.763082 7.6998303 -215.08701 -215.08701 -171.95586 -190.94799 -282.35718 2.3700991 1153.5427 Loop time of 1.1005e-05 on 1 procs for 0 steps with 1754 atoms 0.0% 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 | | 1.1e-05 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5277.00 ave 5277 max 5277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51178.0 ave 51178 max 51178 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102356.0 ave 102356 max 102356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102356 Ave neighs/atom = 58.355758 Neighbor list builds = 0 Dangerous builds = 0 1754 -11882.4625051083 eV 2.37009911930904 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42