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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -47.077061 0.0000000) to (23.062955 47.077061 10.314067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1501214 5.6492473 6.8760448 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -47.077061 0.0000000) to (23.062955 47.077061 10.314067) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1501214 5.6492473 6.8760448 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -47.077061 0.0000000) to (23.062955 47.077061 10.314067) create_atoms CPU = 0.001 seconds 612 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1200 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4417.5134 0 -4417.5134 12926.105 27 0 -4466.0907 0 -4466.0907 3116.1657 Loop time of 0.77419 on 1 procs for 27 steps with 1200 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 = -4417.51344379092 -4466.08682118 -4466.09066979323 Force two-norm initial, final = 53.642922 0.097414453 Force max component initial, final = 7.7899938 0.0049988033 Final line search alpha, max atom move = 1.0000000 0.0049988033 Iterations, force evaluations = 27 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76801 | 0.76801 | 0.76801 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027968 | 0.0027968 | 0.0027968 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003378 | | | 0.44 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5805.00 ave 5805 max 5805 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: 209712.0 ave 209712 max 209712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209712 Ave neighs/atom = 174.76000 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -4466.0907 0 -4466.0907 3116.1657 22396.711 38 0 -4466.4406 0 -4466.4406 3.9064807 22568.077 Loop time of 0.197403 on 1 procs for 11 steps with 1200 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 = -4466.09066979322 -4466.43736299582 -4466.44061927129 Force two-norm initial, final = 83.467571 0.68843504 Force max component initial, final = 72.521821 0.46202849 Final line search alpha, max atom move = 0.00028366155 0.00013105972 Iterations, force evaluations = 11 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18055 | 0.18055 | 0.18055 | 0.0 | 91.46 Neigh | 0.01262 | 0.01262 | 0.01262 | 0.0 | 6.39 Comm | 0.00073611 | 0.00073611 | 0.00073611 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003501 | | | 1.77 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5805.00 ave 5805 max 5805 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: 207552.0 ave 207552 max 207552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207552 Ave neighs/atom = 172.96000 Neighbor list builds = 1 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.588 | 5.588 | 5.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4466.4406 0 -4466.4406 3.9064807 Loop time of 1.904e-06 on 1 procs for 0 steps with 1200 atoms 157.6% 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 | | 1.904e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5805.00 ave 5805 max 5805 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: 207552.0 ave 207552 max 207552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207552 Ave neighs/atom = 172.96000 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.588 | 5.588 | 5.588 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 -4466.4406 -4466.4406 23.053314 95.189816 10.284205 3.9064807 3.9064807 8.4388571 33.161618 -29.881033 2.745402 1119.7191 Loop time of 2.411e-06 on 1 procs for 0 steps with 1200 atoms 248.9% 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 | | 2.411e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5805.00 ave 5805 max 5805 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103776.0 ave 103776 max 103776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 207552.0 ave 207552 max 207552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207552 Ave neighs/atom = 172.96000 Neighbor list builds = 0 Dangerous builds = 0 1200 -4466.44061927129 eV 2.74540203501502 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01