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 = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -44.403825 0.0000000) to (20.932164 44.403825 5.0767954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1565188 6.0946426 5.0767954 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.403825 0.0000000) to (20.932164 44.403825 5.0767954) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1565188 6.0946426 5.0767954 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.403825 0.0000000) to (20.932164 44.403825 5.0767954) create_atoms CPU = 0.001 seconds 412 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2122.816 0 -2122.816 123169.59 120 0 -2861.3732 0 -2861.3732 5190.0286 Loop time of 2.66676 on 1 procs for 120 steps with 816 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 = -2122.81598768116 -2861.37080200681 -2861.37322773454 Force two-norm initial, final = 1192.4124 0.16398757 Force max component initial, final = 282.79110 0.023631503 Final line search alpha, max atom move = 1.0000000 0.023631503 Iterations, force evaluations = 120 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6267 | 2.6267 | 2.6267 | 0.0 | 98.50 Neigh | 0.016624 | 0.016624 | 0.016624 | 0.0 | 0.62 Comm | 0.01327 | 0.01327 | 0.01327 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01018 | | | 0.38 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6264.00 ave 6264 max 6264 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: 134512.0 ave 134512 max 134512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134512 Ave neighs/atom = 164.84314 Neighbor list builds = 2 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -2861.3732 0 -2861.3732 5190.0286 9437.4392 124 0 -2861.4687 0 -2861.4687 242.21114 9471.9748 Loop time of 0.0712821 on 1 procs for 4 steps with 816 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 = -2861.37322773454 -2861.46693545896 -2861.46867359764 Force two-norm initial, final = 59.989483 2.8636387 Force max component initial, final = 52.632384 2.5852630 Final line search alpha, max atom move = 0.00018918289 0.00048908752 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069691 | 0.069691 | 0.069691 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028574 | 0.00028574 | 0.00028574 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001306 | | | 1.83 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241.00 ave 6241 max 6241 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: 133728.0 ave 133728 max 133728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133728 Ave neighs/atom = 163.88235 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2861.4687 0 -2861.4687 242.21114 Loop time of 1.805e-06 on 1 procs for 0 steps with 816 atoms 166.2% 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 | | 1.805e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5407.00 ave 5407 max 5407 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: 125184.0 ave 125184 max 125184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125184 Ave neighs/atom = 153.41176 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.114 | 5.114 | 5.114 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 -2861.4687 -2861.4687 20.999261 88.785427 5.0803642 242.21114 242.21114 438.69676 121.2206 166.71604 2.3790066 800.169 Loop time of 1.761e-06 on 1 procs for 0 steps with 816 atoms 170.4% 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 | | 1.761e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5407.00 ave 5407 max 5407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62592.0 ave 62592 max 62592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 125184.0 ave 125184 max 125184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125184 Ave neighs/atom = 153.41176 Neighbor list builds = 0 Dangerous builds = 0 816 -2861.46867359764 eV 2.37900658599798 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02