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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -42.427043 0.0000000) to (51.962303 42.427043 9.9088223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6133840 6.1712062 6.6058816 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -42.427043 0.0000000) to (51.962303 42.427043 9.9088223) create_atoms CPU = 0.006 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6133840 6.1712062 6.6058816 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -42.427043 0.0000000) to (51.962303 42.427043 9.9088223) create_atoms CPU = 0.005 seconds 1322 atoms in group lower Displacing atoms ... 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2638 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.075 | 6.075 | 6.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8554.5692 0 -8554.5692 30525.013 89 0 -8964.07 0 -8964.07 5492.2899 Loop time of 6.73847 on 1 procs for 89 steps with 2638 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 = -8554.56922769181 -8964.06249632229 -8964.07004550978 Force two-norm initial, final = 240.60787 0.19400945 Force max component initial, final = 34.625787 0.030785786 Final line search alpha, max atom move = 1.0000000 0.030785786 Iterations, force evaluations = 89 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3643 | 6.3643 | 6.3643 | 0.0 | 94.45 Neigh | 0.30138 | 0.30138 | 0.30138 | 0.0 | 4.47 Comm | 0.031121 | 0.031121 | 0.031121 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04167 | | | 0.62 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8887.00 ave 8887 max 8887 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: 377044.0 ave 377044 max 377044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 377044 Ave neighs/atom = 142.92798 Neighbor list builds = 5 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.074 | 6.074 | 6.074 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -8964.07 0 -8964.07 5492.2899 43690.115 99 0 -8965.1379 0 -8965.1379 2.9510377 43980.686 Loop time of 0.642934 on 1 procs for 10 steps with 2638 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8964.07004550983 -8965.13785105518 -8965.13786251205 Force two-norm initial, final = 296.69380 0.42229534 Force max component initial, final = 265.37592 0.14435393 Final line search alpha, max atom move = 0.0013650868 0.00019705565 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62827 | 0.62827 | 0.62827 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026186 | 0.0026186 | 0.0026186 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 1.87 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8899.00 ave 8899 max 8899 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: 376758.0 ave 376758 max 376758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376758 Ave neighs/atom = 142.81956 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.213 | 6.213 | 6.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8965.1379 0 -8965.1379 2.9510377 Loop time of 6.255e-06 on 1 procs for 0 steps with 2638 atoms 223.8% 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 | | 6.255e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8871.00 ave 8871 max 8871 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: 373698.0 ave 373698 max 373698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373698 Ave neighs/atom = 141.65959 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.213 | 6.213 | 6.213 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 -8965.1379 -8965.1379 51.962344 85.606721 9.8870198 2.9510377 2.9510377 0.87484259 2.7311583 5.247112 2.5409965 1790.7806 Loop time of 8.239e-06 on 1 procs for 0 steps with 2638 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 | | 8.239e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8871.00 ave 8871 max 8871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186849.0 ave 186849 max 186849 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 373698.0 ave 373698 max 373698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373698 Ave neighs/atom = 141.65959 Neighbor list builds = 0 Dangerous builds = 0 2638 -8965.13786251205 eV 2.5409965067063 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08