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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -58.990005 0.0000000) to (29.495003 58.990005 3.6584048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9914620 4.9914620 3.6584048 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.990005 0.0000000) to (29.495003 58.990005 3.6584048) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9914620 4.9914620 3.6584048 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.990005 0.0000000) to (29.495003 58.990005 3.6584048) create_atoms CPU = 0.001 seconds 522 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1042 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3915.9741 0 -3915.9741 40469.539 209 0 -4050.5613 0 -4050.5613 384.38412 Loop time of 3.1737 on 1 procs for 209 steps with 1042 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3915.97408074466 -4050.55739546799 -4050.56127668561 Force two-norm initial, final = 314.68536 0.19267391 Force max component initial, final = 95.783170 0.024877899 Final line search alpha, max atom move = 1.0000000 0.024877899 Iterations, force evaluations = 209 408 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1132 | 3.1132 | 3.1132 | 0.0 | 98.09 Neigh | 0.016313 | 0.016313 | 0.016313 | 0.0 | 0.51 Comm | 0.024212 | 0.024212 | 0.024212 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01997 | | | 0.63 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6875.00 ave 6875 max 6875 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: 143312.0 ave 143312 max 143312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143312 Ave neighs/atom = 137.53551 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 209 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -4050.5613 0 -4050.5613 384.38412 12730.593 258 0 -4062.8788 0 -4062.8788 294.38189 12721.193 Loop time of 0.440124 on 1 procs for 49 steps with 1042 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 = -4050.5612766856 -4062.87654715207 -4062.87875189268 Force two-norm initial, final = 369.87080 5.6624037 Force max component initial, final = 268.57750 4.0452039 Final line search alpha, max atom move = 0.00020439827 0.00082683265 Iterations, force evaluations = 49 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38284 | 0.38284 | 0.38284 | 0.0 | 86.99 Neigh | 0.041065 | 0.041065 | 0.041065 | 0.0 | 9.33 Comm | 0.0033022 | 0.0033022 | 0.0033022 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01291 | | | 2.93 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6883.00 ave 6883 max 6883 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: 146264.0 ave 146264 max 146264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146264 Ave neighs/atom = 140.36852 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4062.8788 0 -4062.8788 294.38189 Loop time of 1.999e-06 on 1 procs for 0 steps with 1042 atoms 150.1% 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 | | 1.999e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6888.00 ave 6888 max 6888 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: 146280.0 ave 146280 max 146280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146280 Ave neighs/atom = 140.38388 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 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 -4062.8788 -4062.8788 29.615451 112.59547 3.8149474 294.38189 294.38189 129.23192 486.22293 267.69082 2.2157496 436.80948 Loop time of 2.084e-06 on 1 procs for 0 steps with 1042 atoms 239.9% 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 | | 2.084e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6888.00 ave 6888 max 6888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73140.0 ave 73140 max 73140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146280.0 ave 146280 max 146280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146280 Ave neighs/atom = 140.38388 Neighbor list builds = 0 Dangerous builds = 0 1042 -4062.87875189267 eV 2.21574955761453 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03