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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -31.225699 0.0000000) to (6.3733373 31.225699 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8240024 4.1630465 4.6544275 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.225699 0.0000000) to (6.3733373 31.225699 6.9816412) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8240024 4.1630465 4.6544275 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -31.225699 0.0000000) to (6.3733373 31.225699 6.9816412) create_atoms CPU = 0.000 seconds 122 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 236 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1001.6924 0 -1001.6924 -7056.7226 36 0 -1006.5472 0 -1006.5472 -19009.641 Loop time of 0.977061 on 1 procs for 36 steps with 236 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 = -1001.6923566451 -1006.54622206238 -1006.54716132072 Force two-norm initial, final = 7.6098435 0.093219953 Force max component initial, final = 2.1455914 0.010892956 Final line search alpha, max atom move = 1.0000000 0.010892956 Iterations, force evaluations = 36 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97494 | 0.97494 | 0.97494 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010411 | 0.0010411 | 0.0010411 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001081 | | | 0.11 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2060.00 ave 2060 max 2060 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: 15184.0 ave 15184 max 15184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15184 Ave neighs/atom = 64.338983 Neighbor list builds = 0 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1006.5472 0 -1006.5472 -19009.641 2778.8595 43 0 -1006.7399 0 -1006.7399 -1487.7518 2748.6647 Loop time of 0.13069 on 1 procs for 7 steps with 236 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 = -1006.54716132072 -1006.7398849239 -1006.73992455617 Force two-norm initial, final = 49.467028 0.28913611 Force max component initial, final = 38.090287 0.22399015 Final line search alpha, max atom move = 0.0018525420 0.00041495116 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12999 | 0.12999 | 0.12999 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012694 | 0.00012694 | 0.00012694 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005747 | | | 0.44 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2005.00 ave 2005 max 2005 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: 15436.0 ave 15436 max 15436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15436 Ave neighs/atom = 65.406780 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1006.7399 0 -1006.7399 -1487.7518 Loop time of 1.599e-06 on 1 procs for 0 steps with 236 atoms 125.1% 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 | | 1.599e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2030.00 ave 2030 max 2030 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: 15516.0 ave 15516 max 15516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15516 Ave neighs/atom = 65.745763 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.567 | 4.567 | 4.567 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 -1006.7399 -1006.7399 6.3429763 62.451398 6.9388343 -1487.7518 -1487.7518 129.94025 -4640.5056 47.309819 2.2997858 269.77267 Loop time of 1.364e-06 on 1 procs for 0 steps with 236 atoms 146.6% 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 | | 1.364e-06 | | |100.00 Nlocal: 236.000 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2030.00 ave 2030 max 2030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7758.00 ave 7758 max 7758 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15516.0 ave 15516 max 15516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15516 Ave neighs/atom = 65.745763 Neighbor list builds = 0 Dangerous builds = 0 236 -1006.73992455617 eV 2.2997857848554 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01