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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -47.270522 0.0000000) to (33.425307 47.270522 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 684 atoms using lattice units in orthogonal box = (0.0000000 -47.270522 0.0000000) to (33.425307 47.270522 5.0973115) create_atoms CPU = 0.002 seconds 684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.270522 0.0000000) to (33.425307 47.270522 5.0973115) create_atoms CPU = 0.002 seconds 692 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1376 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_492310898779_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5724.8609 0 -5724.8609 23962.295 580 0 -5864.3729 0 -5864.3729 -9530.6098 Loop time of 50.4585 on 1 procs for 580 steps with 1376 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 = -5724.86087485895 -5864.36732678278 -5864.3728522673 Force two-norm initial, final = 97.429953 0.21806059 Force max component initial, final = 19.969588 0.045804863 Final line search alpha, max atom move = 1.0000000 0.045804863 Iterations, force evaluations = 580 1063 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.17 | 50.17 | 50.17 | 0.0 | 99.43 Neigh | 0.15425 | 0.15425 | 0.15425 | 0.0 | 0.31 Comm | 0.065958 | 0.065958 | 0.065958 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06857 | | | 0.14 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5700.00 ave 5700 max 5700 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: 90178.0 ave 90178 max 90178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90178 Ave neighs/atom = 65.536337 Neighbor list builds = 20 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 580 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.668 | 4.668 | 4.668 Mbytes Step Temp E_pair E_mol TotEng Press Volume 580 0 -5864.3729 0 -5864.3729 -9530.6098 16107.827 608 0 -5874.8377 0 -5874.8377 -11.47648 16001.113 Loop time of 1.35874 on 1 procs for 28 steps with 1376 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 = -5864.37285226728 -5874.83331020208 -5874.83772330068 Force two-norm initial, final = 650.09796 1.9891647 Force max component initial, final = 607.70717 1.1965248 Final line search alpha, max atom move = 0.00010266494 0.00012284115 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3422 | 1.3422 | 1.3422 | 0.0 | 98.78 Neigh | 0.0074201 | 0.0074201 | 0.0074201 | 0.0 | 0.55 Comm | 0.0015287 | 0.0015287 | 0.0015287 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007627 | | | 0.56 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5820.00 ave 5820 max 5820 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: 90264.0 ave 90264 max 90264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90264 Ave neighs/atom = 65.598837 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.807 | 4.807 | 4.807 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5874.8377 0 -5874.8377 -11.47648 Loop time of 1.903e-06 on 1 procs for 0 steps with 1376 atoms 157.6% 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 | | 1.903e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5840.00 ave 5840 max 5840 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: 90220.0 ave 90220 max 90220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90220 Ave neighs/atom = 65.566860 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.807 | 4.807 | 4.807 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 -5874.8377 -5874.8377 33.697495 95.787508 4.9572829 -11.47648 -11.47648 -120.78252 48.37763 37.975449 2.3239314 1905.2719 Loop time of 1.882e-06 on 1 procs for 0 steps with 1376 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5840.00 ave 5840 max 5840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45110.0 ave 45110 max 45110 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90220.0 ave 90220 max 90220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90220 Ave neighs/atom = 65.566860 Neighbor list builds = 0 Dangerous builds = 0 1376 -5874.83772330068 eV 2.32393135831608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:52