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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7265854 4.5554708 5.1120000 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) create_atoms CPU = 0.004 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7265854 4.5554708 5.1120000 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.628669 0.0000000) to (36.506982 51.628669 5.1120000) create_atoms CPU = 0.004 seconds 821 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 1621 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_887933271505_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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5649.6738 0 -5649.6738 12256.677 41 0 -5716.2862 0 -5716.2862 -508.6633 Loop time of 2.30173 on 1 procs for 41 steps with 1621 atoms 58.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5649.6738240999 -5716.28615163584 -5716.28615163584 Force two-norm initial, final = 91.918021 0.23619413 Force max component initial, final = 15.555251 0.038556861 Final line search alpha, max atom move = 1.1920929e-07 4.5963360e-09 Iterations, force evaluations = 41 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2602 | 2.2602 | 2.2602 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02202 | 0.02202 | 0.02202 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01948 | | | 0.85 Nlocal: 1621.00 ave 1621 max 1621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5901.00 ave 5901 max 5901 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: 87230.0 ave 87230 max 87230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87230 Ave neighs/atom = 53.812461 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -5716.2862 0 -5716.2862 -508.6633 19270.266 45 0 -5716.4045 0 -5716.4045 -421.78302 19268.754 Loop time of 0.110072 on 1 procs for 4 steps with 1621 atoms 62.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5716.28615163584 -5716.3988423803 -5716.40454990963 Force two-norm initial, final = 50.640003 9.0551613 Force max component initial, final = 41.580431 6.7927430 Final line search alpha, max atom move = 0.00013346747 0.00090661020 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10551 | 0.10551 | 0.10551 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092558 | 0.00092558 | 0.00092558 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003635 | | | 3.30 Nlocal: 1621.00 ave 1621 max 1621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5973.00 ave 5973 max 5973 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: 87574.0 ave 87574 max 87574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87574 Ave neighs/atom = 54.024676 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.856 | 4.856 | 4.856 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 5717.0008 0 5717.0008 -421.78302 Loop time of 6.585e-06 on 1 procs for 0 steps with 1621 atoms 121.5% 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 | | 6.585e-06 | | |100.00 Nlocal: 1621.00 ave 1621 max 1621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5966.00 ave 5966 max 5966 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: 87592.0 ave 87592 max 87592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87592 Ave neighs/atom = 54.035780 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.856 | 4.856 | 4.856 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 5717.0008 -5716.4045 36.609453 102.87929 5.1160222 -421.78302 -421.78302 -374.20466 -562.74151 -328.40288 2.2783954 693.73608 Loop time of 6.796e-06 on 1 procs for 0 steps with 1621 atoms 191.3% 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 | | 6.796e-06 | | |100.00 Nlocal: 1621.00 ave 1621 max 1621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5966.00 ave 5966 max 5966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43796.0 ave 43796 max 43796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87592.0 ave 87592 max 87592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87592 Ave neighs/atom = 54.035780 Neighbor list builds = 0 Dangerous builds = 0 1621 5717.00082011786 eV 2.2783953688658 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02