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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -31.472000 0.0000000) to (3.1472000 31.472000 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1472000 3.1472000 3.1472000 Created 20 atoms using lattice units in orthogonal box = (0.0000000 -31.472000 0.0000000) to (3.1472000 31.472000 3.1472000) create_atoms CPU = 0.002 seconds 20 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1472000 3.1472000 3.1472000 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -31.472000 0.0000000) to (3.1472000 31.472000 3.1472000) create_atoms CPU = 0.000 seconds 21 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 2 21 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 40 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_424746498193_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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.348 | 4.348 | 4.348 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -272.8 0 -272.8 -0.0081219162 1 0 -272.8 0 -272.8 -0.0081219162 Loop time of 0.00296779 on 1 procs for 1 steps with 40 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -272.800003181171 -272.800003181171 -272.800003181172 Force two-norm initial, final = 6.9472019e-08 2.1045661e-08 Force max component initial, final = 4.4075373e-08 1.3268182e-08 Final line search alpha, max atom move = 1.0000000 1.3268182e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0025632 | 0.0025632 | 0.0025632 | 0.0 | 86.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010026 | 0.00010026 | 0.00010026 | 0.0 | 3.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003043 | | | 10.25 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 928.000 ave 928 max 928 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: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2320 Ave neighs/atom = 58.000000 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.348 | 4.348 | 4.348 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -272.8 0 -272.8 -0.0081219162 623.45199 2 0 -272.8 0 -272.8 1.4191637e-06 623.45198 Loop time of 0.00359727 on 1 procs for 1 steps with 40 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 = -272.800003181172 -272.800003181172 -272.800003181171 Force two-norm initial, final = 5.4749785e-06 6.2937275e-08 Force max component initial, final = 3.2392291e-06 4.7891894e-08 Final line search alpha, max atom move = 1.0000000 4.7891894e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0030187 | 0.0030187 | 0.0030187 | 0.0 | 83.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010986 | 0.00010986 | 0.00010986 | 0.0 | 3.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004687 | | | 13.03 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 928.000 ave 928 max 928 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: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2320 Ave neighs/atom = 58.000000 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -272.8 0 -272.8 1.4191637e-06 Loop time of 1.1006e-05 on 1 procs for 0 steps with 40 atoms 172.6% 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 | | 1.101e-05 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 928.000 ave 928 max 928 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: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2320 Ave neighs/atom = 58.000000 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.486 | 4.486 | 4.486 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 -272.8 -272.8 3.1472 62.943999 3.1472 1.4191637e-06 1.4191637e-06 6.3666164e-05 -0.00012307486 6.366619e-05 2.7255551 1.2930423e-17 Loop time of 1.0945e-05 on 1 procs for 0 steps with 40 atoms 237.6% 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 | | 1.095e-05 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2320 Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 40 -272.800003181171 eV 2.72555512500292 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42