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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -49.602864 0.0000000) to (20.249115 49.602864 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8597877 4.2986667 4.6763329 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.602864 0.0000000) to (20.249115 49.602864 7.0144993) create_atoms CPU = 0.004 seconds 601 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8597877 4.2986667 4.6763329 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.602864 0.0000000) to (20.249115 49.602864 7.0144993) create_atoms CPU = 0.003 seconds 601 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 36 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1195 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5026.6861 0 -5026.6861 18511.358 86 0 -5104.9602 0 -5104.9602 -1193.6645 Loop time of 10.9049 on 1 procs for 86 steps with 1195 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 = -5026.68609705297 -5104.95614964535 -5104.96018505635 Force two-norm initial, final = 95.557271 0.23605465 Force max component initial, final = 20.875195 0.073975318 Final line search alpha, max atom move = 1.0000000 0.073975318 Iterations, force evaluations = 86 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.853 | 10.853 | 10.853 | 0.0 | 99.53 Neigh | 0.013798 | 0.013798 | 0.013798 | 0.0 | 0.13 Comm | 0.01545 | 0.01545 | 0.01545 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0225 | | | 0.21 Nlocal: 1195.00 ave 1195 max 1195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3930.00 ave 3930 max 3930 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: 69610.0 ave 69610 max 69610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69610 Ave neighs/atom = 58.251046 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -5104.9602 0 -5104.9602 -1193.6645 14090.924 88 0 -5104.9702 0 -5104.9702 615.36693 14076.2 Loop time of 0.32479 on 1 procs for 2 steps with 1195 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 = -5104.96018505635 -5104.97014087497 -5104.97019061221 Force two-norm initial, final = 26.783178 0.25495245 Force max component initial, final = 20.116879 0.070971527 Final line search alpha, max atom move = 0.0010307313 7.3152575e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32247 | 0.32247 | 0.32247 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045105 | 0.00045105 | 0.00045105 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001874 | | | 0.58 Nlocal: 1195.00 ave 1195 max 1195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4013.00 ave 4013 max 4013 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: 69672.0 ave 69672 max 69672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69672 Ave neighs/atom = 58.302929 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.717 | 4.717 | 4.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5104.9702 0 -5104.9702 615.36693 Loop time of 6.546e-06 on 1 procs for 0 steps with 1195 atoms 183.3% 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 | | 6.546e-06 | | |100.00 Nlocal: 1195.00 ave 1195 max 1195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4013.00 ave 4013 max 4013 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: 69674.0 ave 69674 max 69674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69674 Ave neighs/atom = 58.304603 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.717 | 4.717 | 4.717 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 -5104.9702 -5104.9702 20.240236 99.205727 7.0102434 615.36693 615.36693 -7.5036168 1853.8007 -0.19628361 2.2590349 744.61598 Loop time of 6.475e-06 on 1 procs for 0 steps with 1195 atoms 308.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 1195.00 ave 1195 max 1195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4013.00 ave 4013 max 4013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34837.0 ave 34837 max 34837 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69674.0 ave 69674 max 69674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69674 Ave neighs/atom = 58.304603 Neighbor list builds = 0 Dangerous builds = 0 1195 -5104.97019061221 eV 2.25903491126816 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11