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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -43.971262 0.0000000) to (53.853577 43.971262 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1640416 5.4211144 5.9426050 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -43.971262 0.0000000) to (53.853577 43.971262 8.9139075) create_atoms CPU = 0.002 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1640416 5.4211144 5.9426050 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.971262 0.0000000) to (53.853577 43.971262 8.9139075) create_atoms CPU = 0.002 seconds 1754 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3478 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_945691923444_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.384 | 7.384 | 7.384 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8377.9414 0 -8377.9414 166471.26 93 0 -11375.642 0 -11375.642 -3345.603 Loop time of 4.08718 on 1 procs for 93 steps with 3478 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 = -8377.94135557624 -11375.632519997 -11375.6419083816 Force two-norm initial, final = 3941.4108 0.24179351 Force max component initial, final = 749.73860 0.0094317761 Final line search alpha, max atom move = 1.0000000 0.0094317761 Iterations, force evaluations = 93 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8963 | 3.8963 | 3.8963 | 0.0 | 95.33 Neigh | 0.14998 | 0.14998 | 0.14998 | 0.0 | 3.67 Comm | 0.016515 | 0.016515 | 0.016515 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02434 | | | 0.60 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11423.0 ave 11423 max 11423 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: 610292.0 ave 610292 max 610292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610292 Ave neighs/atom = 175.47211 Neighbor list builds = 4 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -11375.642 0 -11375.642 -3345.603 42216.439 96 0 -11375.801 0 -11375.801 -150.6735 42122.325 Loop time of 0.145102 on 1 procs for 3 steps with 3478 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 = -11375.6419083816 -11375.7920901081 -11375.8007963718 Force two-norm initial, final = 162.67061 9.2562002 Force max component initial, final = 131.52700 7.6835188 Final line search alpha, max atom move = 3.4917976e-05 0.00026829292 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14227 | 0.14227 | 0.14227 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043241 | 0.00043241 | 0.00043241 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002395 | | | 1.65 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11593.0 ave 11593 max 11593 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: 610464.0 ave 610464 max 610464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610464 Ave neighs/atom = 175.52156 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.526 | 7.526 | 7.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11375.801 0 -11375.801 -150.6735 Loop time of 2.095e-06 on 1 procs for 0 steps with 3478 atoms 190.9% 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 | | 2.095e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11593.0 ave 11593 max 11593 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: 610922.0 ave 610922 max 610922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610922 Ave neighs/atom = 175.65325 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.526 | 7.526 | 7.526 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 -11375.801 -11375.801 53.83646 87.746201 8.916769 -150.6735 -150.6735 32.911807 -291.60004 -193.33227 2.367439 1506.6648 Loop time of 2.164e-06 on 1 procs for 0 steps with 3478 atoms 277.3% 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 | | 2.164e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11593.0 ave 11593 max 11593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 305461.0 ave 305461 max 305461 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 610922.0 ave 610922 max 610922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610922 Ave neighs/atom = 175.65325 Neighbor list builds = 0 Dangerous builds = 0 3478 -11375.8007963718 eV 2.36743901101932 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04