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 4.032082033157349*${_u_distance} variable lattice_constant_converted equal 4.032082033157349*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 65.63754004652543*${_u_distance} variable xmax_converted equal 65.63754004652543*1 variable ymin_converted equal -65.6415721285586*${_u_distance} variable ymin_converted equal -65.6415721285586*1 variable ymax_converted equal 65.6415721285586*${_u_distance} variable ymax_converted equal 65.6415721285586*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082033157349*${_u_distance} variable zmax_converted equal 4.032082033157349*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208203315735 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 65.6375400465254 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6375400465254 -65.6415721285586 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6375400465254 -65.6415721285586 65.6415721285586 ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6375400465254 -65.6415721285586 65.6415721285586 0 ${zmax_converted} units box region whole block 0 65.6375400465254 -65.6415721285586 65.6415721285586 0 4.03208203315735 units box create_box 2 whole Created orthogonal box = (0 -65.6416 0) to (65.6375 65.6416 4.03208) 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 65.6415721285586 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69684 5.69684 4.03208 create_atoms 1 region upper Created 1062 atoms create_atoms CPU = 0.00028491 secs group upper type 1 1062 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.325469268244868 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -65.6415721285586 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 lattice fcc 4.03208203315735 orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69684 5.69684 4.03208 create_atoms 2 region lower Created 1062 atoms create_atoms CPU = 0.000181913 secs group lower type 2 1062 atoms in group lower displace_atoms lower move -7.325469268244868 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 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*4.03208203315735 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604101657867 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 35 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2092 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6990.2019 0 -6990.2019 -642.47357 231 0 -7016.0462 0 -7016.0462 -8061.7533 Loop time of 1.96174 on 1 procs for 231 steps with 2092 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 = -6990.20190501 -7016.04620354 -7016.04620354 Force two-norm initial, final = 22.1637 1.36957e-05 Force max component initial, final = 4.52891 2.04974e-06 Final line search alpha, max atom move = 1 2.04974e-06 Iterations, force evaluations = 231 447 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9115 | 1.9115 | 1.9115 | 0.0 | 97.44 Neigh | 0.0051398 | 0.0051398 | 0.0051398 | 0.0 | 0.26 Comm | 0.027223 | 0.027223 | 0.027223 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01788 | | | 0.91 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12167 ave 12167 max 12167 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: 234360 ave 234360 max 234360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234360 Ave neighs/atom = 112.027 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) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 231 0 -7016.0462 0 -7016.0462 -8061.7533 34744.865 1231 0 -7016.456 0 -7016.456 -2974.7333 34522.349 Loop time of 9.50971 on 1 procs for 1000 steps with 2092 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 = -7016.04620354 -7016.45597449 -7016.45597498 Force two-norm initial, final = 179.109 0.0435169 Force max component initial, final = 134.907 0.0322405 Final line search alpha, max atom move = 0.0290412 0.000936303 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9554 | 8.9554 | 8.9554 | 0.0 | 94.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12004 | 0.12004 | 0.12004 | 0.0 | 1.26 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4343 | | | 4.57 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12104 ave 12104 max 12104 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: 223552 ave 223552 max 223552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223552 Ave neighs/atom = 106.86 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.768 | 5.768 | 5.768 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7016.456 0 -7016.456 -2974.7333 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12115 ave 12115 max 12115 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: 237712 ave 237712 max 237712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237712 Ave neighs/atom = 113.629 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) = 5.768 | 5.768 | 5.768 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 -7016.456 -7016.456 65.407197 131.28314 4.0203682 -2974.7333 -2974.7333 -1.4910235 -8923.5557 0.84691289 2.618462 272.28947 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12115 ave 12115 max 12115 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118856 ave 118856 max 118856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237712 ave 237712 max 237712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237712 Ave neighs/atom = 113.629 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.0209/numatoms.out 2092 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.45597498022-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.45597498022-2092*${isolated_atom_energy} variable adjusted_pe_metal equal -7016.45597498022-2092*0 print "${adjusted_pe_metal} eV" file output/dump_085.0209/energy.out -7016.45597498022 eV print "${mindist_metal} Angstroms" file output/dump_085.0209/mindistance.out 2.61846197836912 Angstroms write_dump all cfg output/dump_085.0209/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_085.0209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11