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 -34.042173 0.0000000) to (11.347391 34.042173 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3643811 4.3643811 3.1472000 Created 78 atoms using lattice units in orthogonal box = (0.0000000 -34.042173 0.0000000) to (11.347391 34.042173 3.1472000) create_atoms CPU = 0.002 seconds 78 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3643811 4.3643811 3.1472000 Created 79 atoms using lattice units in orthogonal box = (0.0000000 -34.042173 0.0000000) to (11.347391 34.042173 3.1472000) create_atoms CPU = 0.001 seconds 79 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 = 4 22 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 = 157 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 = 4 22 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) = 4.374 | 4.374 | 4.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -724.57743 0 -724.57743 242458.76 94 0 -1061.768 0 -1061.768 27869.797 Loop time of 0.341253 on 1 procs for 94 steps with 157 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 = -724.577434542131 -1061.76717870753 -1061.76799507831 Force two-norm initial, final = 561.42955 0.11625368 Force max component initial, final = 222.32719 0.036502009 Final line search alpha, max atom move = 1.0000000 0.036502009 Iterations, force evaluations = 94 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32606 | 0.32606 | 0.32606 | 0.0 | 95.55 Neigh | 0.0042382 | 0.0042382 | 0.0042382 | 0.0 | 1.24 Comm | 0.0066619 | 0.0066619 | 0.0066619 | 0.0 | 1.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004289 | | | 1.26 Nlocal: 157.000 ave 157 max 157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1804.00 ave 1804 max 1804 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: 9320.00 ave 9320 max 9320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9320 Ave neighs/atom = 59.363057 Neighbor list builds = 2 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 = 4 22 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.372 | 4.372 | 4.372 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -1061.768 0 -1061.768 27869.797 2431.4627 107 0 -1062.2467 0 -1062.2467 -46.696562 2452.507 Loop time of 0.0310411 on 1 procs for 13 steps with 157 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1061.76799507831 -1062.24592813832 -1062.2466575755 Force two-norm initial, final = 89.825565 0.80258748 Force max component initial, final = 84.735613 0.27718781 Final line search alpha, max atom move = 0.00055389978 0.00015353426 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028708 | 0.028708 | 0.028708 | 0.0 | 92.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054223 | 0.00054223 | 0.00054223 | 0.0 | 1.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001791 | | | 5.77 Nlocal: 157.000 ave 157 max 157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1610.00 ave 1610 max 1610 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: 9288.00 ave 9288 max 9288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9288 Ave neighs/atom = 59.159236 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 = 4 23 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1062.2467 0 -1062.2467 -46.696562 Loop time of 6.535e-06 on 1 procs for 0 steps with 157 atoms 168.3% 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 | | 6.535e-06 | | |100.00 Nlocal: 157.000 ave 157 max 157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1607.00 ave 1607 max 1607 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: 9206.00 ave 9206 max 9206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9206 Ave neighs/atom = 58.636943 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 = 4 23 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) = 4.510 | 4.510 | 4.510 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 -1062.2467 -1062.2467 11.319921 68.933726 3.1429329 -46.696562 -46.696562 12.045934 -183.34062 31.205004 2.4956246 137.6032 Loop time of 6.415e-06 on 1 procs for 0 steps with 157 atoms 233.8% 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 | | 6.415e-06 | | |100.00 Nlocal: 157.000 ave 157 max 157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1607.00 ave 1607 max 1607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4603.00 ave 4603 max 4603 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9206.00 ave 9206 max 9206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9206 Ave neighs/atom = 58.636943 Neighbor list builds = 0 Dangerous builds = 0 157 -1062.2466575755 eV 2.49562456083725 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