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 (15.736000 31.472000 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4060800 4.4060800 3.1472000 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -31.472000 0.0000000) to (15.736000 31.472000 3.1472000) create_atoms CPU = 0.001 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4060800 4.4060800 3.1472000 Created 101 atoms using lattice units in orthogonal box = (0.0000000 -31.472000 0.0000000) to (15.736000 31.472000 3.1472000) create_atoms CPU = 0.001 seconds 101 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 = 6 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 0 atoms, new total = 201 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 = 6 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) = 4.382 | 4.382 | 4.382 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1217.0316 0 -1217.0316 148372.21 60 0 -1359.6862 0 -1359.6862 17634.814 Loop time of 0.320846 on 1 procs for 60 steps with 201 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 = -1217.03156767782 -1359.68551272714 -1359.68622013301 Force two-norm initial, final = 313.76188 0.11890190 Force max component initial, final = 115.39116 0.030359005 Final line search alpha, max atom move = 1.0000000 0.030359005 Iterations, force evaluations = 60 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31032 | 0.31032 | 0.31032 | 0.0 | 96.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0060194 | 0.0060194 | 0.0060194 | 0.0 | 1.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004503 | | | 1.40 Nlocal: 201.000 ave 201 max 201 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1964.00 ave 1964 max 1964 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: 11876.0 ave 11876 max 11876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11876 Ave neighs/atom = 59.084577 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 = 6 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.382 | 4.382 | 4.382 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1359.6862 0 -1359.6862 17634.814 3117.2599 71 0 -1360.057 0 -1360.057 254.31943 3134.0668 Loop time of 0.0408622 on 1 procs for 11 steps with 201 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 = -1359.68622013301 -1360.05691945047 -1360.05698149385 Force two-norm initial, final = 82.658309 1.0347712 Force max component initial, final = 79.759367 0.61953051 Final line search alpha, max atom move = 0.0021418848 0.0013269630 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037607 | 0.037607 | 0.037607 | 0.0 | 92.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069278 | 0.00069278 | 0.00069278 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002562 | | | 6.27 Nlocal: 201.000 ave 201 max 201 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1944.00 ave 1944 max 1944 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: 11884.0 ave 11884 max 11884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11884 Ave neighs/atom = 59.124378 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 = 6 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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1360.057 0 -1360.057 254.31943 Loop time of 8.56e-06 on 1 procs for 0 steps with 201 atoms 163.6% 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 | | 8.56e-06 | | |100.00 Nlocal: 201.000 ave 201 max 201 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1937.00 ave 1937 max 1937 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: 11820.0 ave 11820 max 11820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11820 Ave neighs/atom = 58.805970 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 = 6 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) = 4.520 | 4.520 | 4.520 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 -1360.057 -1360.057 15.722963 63.548978 3.1366444 254.31943 254.31943 316.44983 218.75582 227.75264 2.4781086 156.38818 Loop time of 1.1035e-05 on 1 procs for 0 steps with 201 atoms 145.0% 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 | | 1.103e-05 | | |100.00 Nlocal: 201.000 ave 201 max 201 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1937.00 ave 1937 max 1937 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5910.00 ave 5910 max 5910 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11820.0 ave 11820 max 11820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11820 Ave neighs/atom = 58.805970 Neighbor list builds = 0 Dangerous builds = 0 201 -1360.05698149385 eV 2.47810862901921 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