LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 3.9946166351437573*${_u_distance} variable lattice_constant_converted equal 3.9946166351437573*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.08342875138339*${_u_distance} variable xmax_converted equal 52.08342875138339*1 variable ymin_converted equal -52.087423368018534*${_u_distance} variable ymin_converted equal -52.087423368018534*1 variable ymax_converted equal 52.087423368018534*${_u_distance} variable ymax_converted equal 52.087423368018534*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946166351437573*${_u_distance} variable zmax_converted equal 3.9946166351437573*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99461663514376 Lattice spacing in x,y,z = 3.99462 3.99462 3.99462 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.0834287513834 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.0834287513834 -52.0874233680185 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.0834287513834 -52.0874233680185 52.0874233680185 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.0834287513834 -52.0874233680185 52.0874233680185 0 ${zmax_converted} units box region whole block 0 52.0834287513834 -52.0874233680185 52.0874233680185 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -52.0874 0) to (52.0834 52.0874 3.99462) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 52.0874233680185 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.28922 4.28922 3.99462 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000264883 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.867282164682384 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.0874233680185 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.28922 4.28922 3.99462 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000148058 secs group lower type 2 682 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*3.99461663514376 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730831757188 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 14 28 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1340 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4377.6302 0 -4377.6302 -28.740927 92 0 -4391.9762 0 -4391.9762 -4805.144 Loop time of 1.85884 on 1 procs for 92 steps with 1340 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4377.63018548 -4391.97622969 -4391.97622969 Force two-norm initial, final = 11.6193 0.00832675 Force max component initial, final = 2.76738 0.00128011 Final line search alpha, max atom move = 0.00012207 1.56264e-07 Iterations, force evaluations = 92 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8384 | 1.8384 | 1.8384 | 0.0 | 98.90 Neigh | 0.004153 | 0.004153 | 0.004153 | 0.0 | 0.22 Comm | 0.010167 | 0.010167 | 0.010167 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006099 | | | 0.33 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8533 ave 8533 max 8533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172976 ave 172976 max 172976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172976 Ave neighs/atom = 129.087 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -4391.9762 0 -4391.9762 -4805.144 21673.924 99 0 -4392.2035 0 -4392.2035 -1410.8144 21483.486 Loop time of 0.309713 on 1 procs for 7 steps with 1340 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4391.97622969 -4392.20348295 -4392.20348295 Force two-norm initial, final = 71.8074 0.0692342 Force max component initial, final = 51.4942 0.00866998 Final line search alpha, max atom move = 2.53795e-06 2.20039e-08 Iterations, force evaluations = 7 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30282 | 0.30282 | 0.30282 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016751 | 0.0016751 | 0.0016751 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005216 | | | 1.68 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8501 ave 8501 max 8501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174312 ave 174312 max 174312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174312 Ave neighs/atom = 130.084 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal -6.30324000329931e-20 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.206 | 5.206 | 5.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4392.2035 0 -4392.2035 -1410.8144 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8542 ave 8542 max 8542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174992 ave 174992 max 174992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174992 Ave neighs/atom = 130.591 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 5.206 | 5.206 | 5.206 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 -4392.2035 -4392.2035 51.881435 104.17485 3.9749338 -1410.8144 -1410.8144 0.16999317 -4233.2065 0.59333469 2.536145 194.98966 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1340 atoms 0.0% 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 | | 2.146e-06 | | |100.00 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8542 ave 8542 max 8542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87496 ave 87496 max 87496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174992 ave 174992 max 174992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174992 Ave neighs/atom = 130.591 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.7974/numatoms.out 1340 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4392.20348295202-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4392.20348295202-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -4392.20348295202-1340*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4392.20348295202 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.53614503878854 Angstroms write_dump all cfg output/dump_008.7974/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_008.7974/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02