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 = 4.0320827 4.0320827 4.0320827 Created orthogonal box = (0.0000000 -45.080055 0.0000000) to (9.0160110 45.080055 4.0320827) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4096066 5.4096066 4.0320827 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -45.080055 0.0000000) to (9.0160110 45.080055 4.0320827) create_atoms CPU = 0.002 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4096066 5.4096066 4.0320827 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -45.080055 0.0000000) to (9.0160110 45.080055 4.0320827) create_atoms CPU = 0.001 seconds 102 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 3 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 7.5580544182181 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 200 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_324507536345_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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -655.75647 0 -655.75647 13390.575 18 0 -669.76119 0 -669.76119 7373.9537 Loop time of 0.209191 on 1 procs for 18 steps with 200 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 = -655.75647069439 -669.760697098619 -669.761188488052 Force two-norm initial, final = 31.980148 0.056717768 Force max component initial, final = 11.304979 0.014332913 Final line search alpha, max atom move = 1.0000000 0.014332913 Iterations, force evaluations = 18 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20406 | 0.20406 | 0.20406 | 0.0 | 97.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029068 | 0.0029068 | 0.0029068 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002228 | | | 1.07 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2639.00 ave 2639 max 2639 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: 26464.0 ave 26464 max 26464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26464 Ave neighs/atom = 132.32000 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -669.76119 0 -669.76119 7373.9537 3277.6177 33 0 -669.9509 0 -669.9509 36.913067 3306.089 Loop time of 0.121205 on 1 procs for 15 steps with 200 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 = -669.761188488051 -669.950668447106 -669.950897374979 Force two-norm initial, final = 32.072119 0.65143862 Force max component initial, final = 30.206678 0.40292838 Final line search alpha, max atom move = 0.0073302552 0.0029535679 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10932 | 0.10932 | 0.10932 | 0.0 | 90.19 Neigh | 0.0043611 | 0.0043611 | 0.0043611 | 0.0 | 3.60 Comm | 0.0016768 | 0.0016768 | 0.0016768 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005848 | | | 4.82 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2639.00 ave 2639 max 2639 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: 25656.0 ave 25656 max 25656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25656 Ave neighs/atom = 128.28000 Neighbor list builds = 1 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -669.9509 0 -669.9509 36.913067 Loop time of 9.282e-06 on 1 procs for 0 steps with 200 atoms 204.7% 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 | | 9.282e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2639.00 ave 2639 max 2639 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: 25160.0 ave 25160 max 25160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25160 Ave neighs/atom = 125.80000 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.552 | 4.552 | 4.552 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 -669.9509 -669.9509 8.9957772 91.418225 4.0201574 36.913067 36.913067 -172.86271 88.914755 194.68716 2.6176001 194.67036 Loop time of 1.0093e-05 on 1 procs for 0 steps with 200 atoms 178.3% 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 | | 1.009e-05 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2639.00 ave 2639 max 2639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12580.0 ave 12580 max 12580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25160.0 ave 25160 max 25160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25160 Ave neighs/atom = 125.80000 Neighbor list builds = 0 Dangerous builds = 0 200 -669.950897374979 eV 2.6176000566763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00