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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -61.076932 0.0000000) to (43.185053 61.076932 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8186925 6.9644521 5.7200000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.076932 0.0000000) to (43.185053 61.076932 5.7200000) create_atoms CPU = 0.003 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8186925 6.9644521 5.7200000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.076932 0.0000000) to (43.185053 61.076932 5.7200000) create_atoms CPU = 0.002 seconds 916 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 38 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1824 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_353977746962_000#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.153 | 5.153 | 5.153 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6058.0138 0 -6058.0138 8801.4183 47 0 -6116.3841 0 -6116.3841 2238.2569 Loop time of 4.67191 on 1 procs for 47 steps with 1824 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 = -6058.01382565407 -6116.37840668852 -6116.38412616005 Force two-norm initial, final = 54.072372 0.19423481 Force max component initial, final = 11.167461 0.019564537 Final line search alpha, max atom move = 1.0000000 0.019564537 Iterations, force evaluations = 47 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6391 | 4.6391 | 4.6391 | 0.0 | 99.30 Neigh | 0.018243 | 0.018243 | 0.018243 | 0.0 | 0.39 Comm | 0.0074201 | 0.0074201 | 0.0074201 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007189 | | | 0.15 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 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: 139904.0 ave 139904 max 139904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139904 Ave neighs/atom = 76.701754 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.153 | 5.153 | 5.153 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -6116.3841 0 -6116.3841 2238.2569 30174.264 49 0 -6116.4049 0 -6116.4049 1028.9671 30220.249 Loop time of 0.275984 on 1 procs for 2 steps with 1824 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 = -6116.38412616006 -6116.40434721318 -6116.40485419153 Force two-norm initial, final = 36.706294 0.19261355 Force max component initial, final = 29.407623 0.017656358 Final line search alpha, max atom move = 0.00039298186 6.9386285e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27443 | 0.27443 | 0.27443 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027945 | 0.00027945 | 0.00027945 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001274 | | | 0.46 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 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: 139936.0 ave 139936 max 139936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139936 Ave neighs/atom = 76.719298 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.291 | 5.291 | 5.291 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6116.4049 0 -6116.4049 1028.9671 Loop time of 1.827e-06 on 1 procs for 0 steps with 1824 atoms 164.2% 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 | | 1.827e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 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: 139808.0 ave 139808 max 139808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139808 Ave neighs/atom = 76.649123 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.291 | 5.291 | 5.291 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 -6116.4049 -6116.4049 43.231822 122.15386 5.7225196 1028.9671 1028.9671 -0.55180124 3087.9891 -0.5360772 2.6298298 833.33719 Loop time of 2.347e-06 on 1 procs for 0 steps with 1824 atoms 170.4% 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 | | 2.347e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69904.0 ave 69904 max 69904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139808.0 ave 139808 max 139808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139808 Ave neighs/atom = 76.649123 Neighbor list builds = 0 Dangerous builds = 0 1824 -6116.40485419153 eV 2.62982978591168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05