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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2417233 6.0184976 5.1068646 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068646) create_atoms CPU = 0.003 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2417233 6.0184976 5.1068646 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -64.999774 0.0000000) to (45.961781 64.999774 5.1068646) 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 ghost atom cutoff = 6 binsize = 3, bins = 16 44 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 = 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_162036141261_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 = 16 44 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) = 5.707 | 5.707 | 5.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10727.466 0 -10727.466 30567.683 750 0 -11058.813 0 -11058.813 4021.1556 Loop time of 109.821 on 1 procs for 750 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 = -10727.4659595617 -11058.8025362504 -11058.8129735993 Force two-norm initial, final = 207.63522 0.33968859 Force max component initial, final = 35.731811 0.089814684 Final line search alpha, max atom move = 0.95126243 0.085437335 Iterations, force evaluations = 750 1351 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 109.07 | 109.07 | 109.07 | 0.0 | 99.31 Neigh | 0.41197 | 0.41197 | 0.41197 | 0.0 | 0.38 Comm | 0.16529 | 0.16529 | 0.16529 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1762 | | | 0.16 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9387.00 ave 9387 max 9387 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: 170882.0 ave 170882 max 170882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170882 Ave neighs/atom = 65.875867 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 ghost atom cutoff = 6 binsize = 3, bins = 16 44 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 : 750 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.322 | 5.322 | 5.322 Mbytes Step Temp E_pair E_mol TotEng Press Volume 750 0 -11058.813 0 -11058.813 4021.1556 30513.571 776 0 -11081.419 0 -11081.419 -10.556782 30542.717 Loop time of 2.00398 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 = -11058.8129735993 -11081.4169177089 -11081.4185410638 Force two-norm initial, final = 1327.5144 2.3980384 Force max component initial, final = 946.09303 0.63834991 Final line search alpha, max atom move = 0.00011579309 7.3916507e-05 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9618 | 1.9618 | 1.9618 | 0.0 | 97.90 Neigh | 0.027013 | 0.027013 | 0.027013 | 0.0 | 1.35 Comm | 0.0025882 | 0.0025882 | 0.0025882 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01255 | | | 0.63 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9556.00 ave 9556 max 9556 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: 170070.0 ave 170070 max 170070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170070 Ave neighs/atom = 65.562837 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 ghost atom cutoff = 6 binsize = 3, bins = 16 45 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11081.419 0 -11081.419 -10.556782 Loop time of 2.015e-06 on 1 procs for 0 steps with 2594 atoms 198.5% 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 | | 2.015e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9618.00 ave 9618 max 9618 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: 170028.0 ave 170028 max 170028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170028 Ave neighs/atom = 65.546646 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 = 16 45 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) = 5.462 | 5.462 | 5.462 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 -11081.419 -11081.419 46.174472 132.84161 4.979338 -10.556782 -10.556782 -25.53197 -34.217933 28.079557 2.3620211 3619.8998 Loop time of 2.259e-06 on 1 procs for 0 steps with 2594 atoms 221.3% 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 | | 2.259e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9618.00 ave 9618 max 9618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85014.0 ave 85014 max 85014 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170028.0 ave 170028 max 170028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170028 Ave neighs/atom = 65.546646 Neighbor list builds = 0 Dangerous builds = 0 2594 -11081.4185410638 eV 2.36202112673597 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:52