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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -56.924823 0.0000000) to (34.859192 56.924823 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6224504 5.5088538 5.9028292 Created 1484 atoms using lattice units in orthogonal box = (0.0000000 -56.924823 0.0000000) to (34.859192 56.924823 8.8542437) create_atoms CPU = 0.002 seconds 1484 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6224504 5.5088538 5.9028292 Created 1490 atoms using lattice units in orthogonal box = (0.0000000 -56.924823 0.0000000) to (34.859192 56.924823 8.8542437) create_atoms CPU = 0.002 seconds 1490 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 13 42 4 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2954 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 13 42 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.134 | 5.134 | 5.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10022.629 0 -10022.629 25365.436 13 0 -10417.845 0 -10417.845 2713.6035 Loop time of 1.18695 on 1 procs for 13 steps with 2954 atoms 43.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -10022.6294446309 -10417.8447218664 -10417.8447218664 Force two-norm initial, final = 514.57747 2.2761389 Force max component initial, final = 102.33483 0.37561931 Final line search alpha, max atom move = 2.2238532e-09 8.3532222e-10 Iterations, force evaluations = 13 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1747 | 1.1747 | 1.1747 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050372 | 0.0050372 | 0.0050372 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007181 | | | 0.61 Nlocal: 2954.00 ave 2954 max 2954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241.00 ave 6241 max 6241 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: 158832.0 ave 158832 max 158832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158832 Ave neighs/atom = 53.768450 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 13 42 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.134 | 5.134 | 5.134 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -10417.845 0 -10417.845 2713.6035 35139.896 16 0 -10417.976 0 -10417.976 452.30468 35197.91 Loop time of 0.0899648 on 1 procs for 3 steps with 2954 atoms 44.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10417.8447218664 -10417.9663562492 -10417.9755927753 Force two-norm initial, final = 118.88274 20.312357 Force max component initial, final = 106.98970 18.431010 Final line search alpha, max atom move = 4.7187562e-05 0.00086971442 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087511 | 0.087511 | 0.087511 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028523 | 0.00028523 | 0.00028523 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002169 | | | 2.41 Nlocal: 2954.00 ave 2954 max 2954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 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: 159172.0 ave 159172 max 159172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159172 Ave neighs/atom = 53.883548 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 13 42 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.272 | 5.272 | 5.272 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 10435.745 0 10435.745 452.30468 Loop time of 2.469e-06 on 1 procs for 0 steps with 2954 atoms 162.0% 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 | | 2.469e-06 | | |100.00 Nlocal: 2954.00 ave 2954 max 2954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 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: 159148.0 ave 159148 max 159148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159148 Ave neighs/atom = 53.875423 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 13 42 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.272 | 5.272 | 5.272 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 10435.745 -10417.976 34.83926 114.10472 8.8540981 452.30468 452.30468 196.42892 840.8423 319.64281 2.2283603 718.37887 Loop time of 2.666e-06 on 1 procs for 0 steps with 2954 atoms 262.6% 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 | | 2.666e-06 | | |100.00 Nlocal: 2954.00 ave 2954 max 2954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301.00 ave 6301 max 6301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79574.0 ave 79574 max 79574 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159148.0 ave 159148 max 159148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159148 Ave neighs/atom = 53.875423 Neighbor list builds = 0 Dangerous builds = 0 2954 10435.7445459673 eV 2.22836031497678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01