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 -38.594754 0.0000000) to (27.290612 38.594754 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2241747 6.0939085 5.1120000 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.594754 0.0000000) to (27.290612 38.594754 5.1120000) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2241747 6.0939085 5.1120000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.594754 0.0000000) to (27.290612 38.594754 5.1120000) create_atoms CPU = 0.003 seconds 458 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 = 10 29 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 0 atoms, new total = 914 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_003#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 = 10 29 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3085.3359 0 -3085.3359 44616.07 90 0 -3245.7389 0 -3245.7389 3111.3941 Loop time of 2.41103 on 1 procs for 90 steps with 914 atoms 47.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3085.33591465638 -3245.73626515361 -3245.73893481077 Force two-norm initial, final = 232.62857 0.15221116 Force max component initial, final = 77.200694 0.017190572 Final line search alpha, max atom move = 1.0000000 0.017190572 Iterations, force evaluations = 90 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.37 | 2.37 | 2.37 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021005 | 0.021005 | 0.021005 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02001 | | | 0.83 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3846.00 ave 3846 max 3846 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: 49860.0 ave 49860 max 49860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49860 Ave neighs/atom = 54.551422 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 = 10 29 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 : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3245.7389 0 -3245.7389 3111.3941 10768.678 93 0 -3245.7811 0 -3245.7811 167.1844 10791.441 Loop time of 0.0701478 on 1 procs for 3 steps with 914 atoms 48.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3245.73893481077 -3245.77875074132 -3245.7810638752 Force two-norm initial, final = 40.827670 2.3744445 Force max component initial, final = 35.975777 1.9148121 Final line search alpha, max atom move = 0.00012855130 0.00024615158 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06762 | 0.06762 | 0.06762 | 0.0 | 96.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056958 | 0.00056958 | 0.00056958 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001958 | | | 2.79 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3802.00 ave 3802 max 3802 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: 50736.0 ave 50736 max 50736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50736 Ave neighs/atom = 55.509847 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 = 10 29 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) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3245.7811 0 -3245.7811 167.1844 Loop time of 6.846e-06 on 1 procs for 0 steps with 914 atoms 116.9% 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 | | 6.846e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3804.00 ave 3804 max 3804 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: 50692.0 ave 50692 max 50692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50692 Ave neighs/atom = 55.461707 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 = 10 29 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) = 4.691 | 4.691 | 4.691 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 -3245.7811 -3245.7811 27.350752 77.211594 5.1100793 167.1844 167.1844 284.91354 206.99111 9.6485531 2.3970624 810.41203 Loop time of 6.826e-06 on 1 procs for 0 steps with 914 atoms 175.8% 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 | | 6.826e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3804.00 ave 3804 max 3804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25346.0 ave 25346 max 25346 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50692.0 ave 50692 max 50692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50692 Ave neighs/atom = 55.461707 Neighbor list builds = 0 Dangerous builds = 0 914 -3245.7810638752 eV 2.39706236919883 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02