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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -36.379699 0.0000000) to (31.505744 36.379699 6.1787847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6548771 5.5968768 6.1787847 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -36.379699 0.0000000) to (31.505744 36.379699 6.1787847) create_atoms CPU = 0.004 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6548771 5.5968768 6.1787847 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.379699 0.0000000) to (31.505744 36.379699 6.1787847) create_atoms CPU = 0.003 seconds 629 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 26 3 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1250 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4783.5361 0 -4783.5361 88906.76 73 0 -5261.3896 0 -5261.3896 58430.945 Loop time of 10.3435 on 1 procs for 73 steps with 1250 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 = -4783.53613461348 -5261.38605191904 -5261.38955752617 Force two-norm initial, final = 547.22453 0.26574374 Force max component initial, final = 101.77125 0.060876467 Final line search alpha, max atom move = 0.84412707 0.051387474 Iterations, force evaluations = 73 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.283 | 10.283 | 10.283 | 0.0 | 99.42 Neigh | 0.027909 | 0.027909 | 0.027909 | 0.0 | 0.27 Comm | 0.013866 | 0.013866 | 0.013866 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01863 | | | 0.18 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4562.00 ave 4562 max 4562 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: 73496.0 ave 73496 max 73496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73496 Ave neighs/atom = 58.796800 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -5261.3896 0 -5261.3896 58430.945 14163.869 86 0 -5266.1873 0 -5266.1873 396.97008 14424.182 Loop time of 1.38553 on 1 procs for 13 steps with 1250 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 = -5261.38955752617 -5266.18674329363 -5266.18728779177 Force two-norm initial, final = 901.39066 6.9439970 Force max component initial, final = 600.09906 4.3473276 Final line search alpha, max atom move = 0.00060282373 0.0026206723 Iterations, force evaluations = 13 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3763 | 1.3763 | 1.3763 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016024 | 0.0016024 | 0.0016024 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007606 | | | 0.55 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4513.00 ave 4513 max 4513 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: 75186.0 ave 75186 max 75186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75186 Ave neighs/atom = 60.148800 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.769 | 4.769 | 4.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5266.1873 0 -5266.1873 396.97008 Loop time of 6.214e-06 on 1 procs for 0 steps with 1250 atoms 193.1% 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 | | 6.214e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4470.00 ave 4470 max 4470 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: 71396.0 ave 71396 max 71396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71396 Ave neighs/atom = 57.116800 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.769 | 4.769 | 4.769 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 -5266.1873 -5266.1873 31.568205 73.567193 6.210937 396.97008 396.97008 483.83991 328.53863 378.5317 2.2678157 1084.3892 Loop time of 6.455e-06 on 1 procs for 0 steps with 1250 atoms 294.3% 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 | | 6.455e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4470.00 ave 4470 max 4470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35698.0 ave 35698 max 35698 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71396.0 ave 71396 max 71396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71396 Ave neighs/atom = 57.116800 Neighbor list builds = 0 Dangerous builds = 0 1250 -5266.18728779177 eV 2.26781571121674 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12