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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2417233 6.0184976 5.1068645 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) create_atoms CPU = 0.003 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2417233 6.0184976 5.1068645 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068645) create_atoms CPU = 0.003 seconds 1299 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2594 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.115 | 6.115 | 6.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10690.026 0 -10690.026 31630.221 836 0 -11055.232 0 -11055.232 5175.3777 Loop time of 332.838 on 1 procs for 836 steps with 2594 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10690.025849445 -11055.2212041085 -11055.2321013164 Force two-norm initial, final = 311.48315 0.35896024 Force max component initial, final = 56.495425 0.098735227 Final line search alpha, max atom move = 0.70993622 0.070095714 Iterations, force evaluations = 836 1555 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 331.71 | 331.71 | 331.71 | 0.0 | 99.66 Neigh | 0.6398 | 0.6398 | 0.6398 | 0.0 | 0.19 Comm | 0.25695 | 0.25695 | 0.25695 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2283 | | | 0.07 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11009.0 ave 11009 max 11009 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: 292836.0 ave 292836 max 292836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292836 Ave neighs/atom = 112.88975 Neighbor list builds = 30 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 836 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.731 | 5.731 | 5.731 Mbytes Step Temp E_pair E_mol TotEng Press Volume 836 0 -11055.232 0 -11055.232 5175.3777 30513.57 862 0 -11078.133 0 -11078.133 -16.685445 30558.441 Loop time of 7.42216 on 1 procs for 26 steps with 2594 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11055.2321013164 -11078.1221654907 -11078.1328722364 Force two-norm initial, final = 1343.5085 4.2054801 Force max component initial, final = 953.95959 3.1221102 Final line search alpha, max atom move = 4.3705341e-05 0.00013645289 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3598 | 7.3598 | 7.3598 | 0.0 | 99.16 Neigh | 0.041944 | 0.041944 | 0.041944 | 0.0 | 0.57 Comm | 0.0034609 | 0.0034609 | 0.0034609 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01693 | | | 0.23 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11221.0 ave 11221 max 11221 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: 292328.0 ave 292328 max 292328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292328 Ave neighs/atom = 112.69391 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.872 | 5.872 | 5.872 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11078.133 0 -11078.133 -16.685445 Loop time of 2.572e-06 on 1 procs for 0 steps with 2594 atoms 155.5% 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 | | 2.572e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11274.0 ave 11274 max 11274 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: 292250.0 ave 292250 max 292250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292250 Ave neighs/atom = 112.66384 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.872 | 5.872 | 5.872 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 -11078.133 -11078.133 46.261372 132.72445 4.9769324 -16.685445 -16.685445 -164.75896 32.806994 81.895635 2.3289483 5326.999 Loop time of 2.761e-06 on 1 procs for 0 steps with 2594 atoms 217.3% 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 | | 2.761e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11274.0 ave 11274 max 11274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146125.0 ave 146125 max 146125 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292250.0 ave 292250 max 292250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292250 Ave neighs/atom = 112.66384 Neighbor list builds = 0 Dangerous builds = 0 2594 -11078.1328722363 eV 2.32894830399363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:05:41