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 4.128871455788613*${_u_distance} variable lattice_constant_converted equal 4.128871455788613*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.50933340847812*${_u_distance} variable xmax_converted equal 42.50933340847812*1 variable ymin_converted equal -42.51346227993391*${_u_distance} variable ymin_converted equal -42.51346227993391*1 variable ymax_converted equal 42.51346227993391*${_u_distance} variable ymax_converted equal 42.51346227993391*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.128871455788613*${_u_distance} variable zmax_converted equal 4.128871455788613*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.12887145578861 Lattice spacing in x,y,z = 4.12887 4.12887 4.12887 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 42.5093334084781 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.5093334084781 -42.5134622799339 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.5093334084781 -42.5134622799339 42.5134622799339 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.5093334084781 -42.5134622799339 42.5134622799339 0 ${zmax_converted} units box region whole block 0 42.5093334084781 -42.5134622799339 42.5134622799339 0 4.12887145578861 units box create_box 2 whole Created orthogonal box = (0 -42.5135 0) to (42.5093 42.5135 4.12887) 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 42.5134622799339 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61444 5.61444 4.12887 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.000277996 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.63303356344415 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.5134622799339 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61444 5.61444 4.12887 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 0.000138044 secs group lower type 2 426 atoms in group lower displace_atoms lower move -4.63303356344415 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.12887145578861 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0644357278943 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 19 1 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 834 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.972 | 4.972 | 4.972 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3067.5573 0 -3067.5573 -7888.0265 238 0 -3085.5449 0 -3085.5449 -12973.701 Loop time of 2.52955 on 1 procs for 238 steps with 834 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 = -3067.55731529 -3085.54492501 -3085.54492501 Force two-norm initial, final = 22.0697 1.02399e-05 Force max component initial, final = 6.1258 3.23163e-06 Final line search alpha, max atom move = 1 3.23163e-06 Iterations, force evaluations = 238 461 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4967 | 2.4967 | 2.4967 | 0.0 | 98.70 Neigh | 0.0060139 | 0.0060139 | 0.0060139 | 0.0 | 0.24 Comm | 0.017633 | 0.017633 | 0.017633 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009201 | | | 0.36 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6416 ave 6416 max 6416 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: 148248 ave 148248 max 148248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148248 Ave neighs/atom = 177.755 Neighbor list builds = 2 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) = 4.972 | 4.972 | 4.972 Mbytes Step Temp E_pair E_mol TotEng Press Volume 238 0 -3085.5449 0 -3085.5449 -12973.701 14923.549 1238 0 -3086.183 0 -3086.183 -1680.8575 14756.493 Loop time of 11.5077 on 1 procs for 1000 steps with 834 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3085.54492501 -3086.18296799 -3086.18296802 Force two-norm initial, final = 159.53 0.0173511 Force max component initial, final = 115.319 0.0158536 Final line search alpha, max atom move = 0.221856 0.00351721 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.217 | 11.217 | 11.217 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067495 | 0.067495 | 0.067495 | 0.0 | 0.59 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2233 | | | 1.94 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6431 ave 6431 max 6431 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: 148060 ave 148060 max 148060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148060 Ave neighs/atom = 177.53 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 0.0 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3086.183 0 -3086.183 -1680.8575 Loop time of 1.19209e-06 on 1 procs for 0 steps with 834 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 | | 1.192e-06 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6446 ave 6446 max 6446 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: 153472 ave 153472 max 153472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153472 Ave neighs/atom = 184.019 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) = 5.105 | 5.105 | 5.105 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 -3086.183 -3086.183 42.270622 85.026925 4.105708 -1680.8575 -1680.8575 0.19374315 -5044.478 1.7116325 2.6086745 727.9078 Loop time of 1.90735e-06 on 1 procs for 0 steps with 834 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 | | 1.907e-06 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6446 ave 6446 max 6446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76736 ave 76736 max 76736 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 153472 ave 153472 max 153472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153472 Ave neighs/atom = 184.019 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_058.1092/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3086.18296801526-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3086.18296801526-834*${isolated_atom_energy} variable adjusted_pe_metal equal -3086.18296801526-834*0 print "${adjusted_pe_metal} eV" file output/dump_058.1092/energy.out -3086.18296801526 eV print "${mindist_metal} Angstroms" file output/dump_058.1092/mindistance.out 2.60867445053318 Angstroms write_dump all cfg output/dump_058.1092/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_058.1092/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:14