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 4.081654928624631*${_u_distance} variable lattice_constant_converted equal 4.081654928624631*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 81.01853701967286*${_u_distance} variable xmax_converted equal 81.01853701967286*1 variable ymin_converted equal -81.02261867460149*${_u_distance} variable ymin_converted equal -81.02261867460149*1 variable ymax_converted equal 81.02261867460149*${_u_distance} variable ymax_converted equal 81.02261867460149*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.081654928624631*${_u_distance} variable zmax_converted equal 4.081654928624631*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.08165492862463 Lattice spacing in x,y,z = 4.08165 4.08165 4.08165 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 81.0185370196729 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 81.0185370196729 -81.0226186746015 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 81.0185370196729 -81.0226186746015 81.0226186746015 ${zmin_converted} ${zmax_converted} units box region whole block 0 81.0185370196729 -81.0226186746015 81.0226186746015 0 ${zmax_converted} units box region whole block 0 81.0185370196729 -81.0226186746015 81.0226186746015 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -81.0226 0) to (81.0185 81.0226 4.08165) 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 81.0226186746015 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.75766 5.75766 4.08165 create_atoms 1 region upper Created 1577 atoms create_atoms CPU = 0.000555992 secs group upper type 1 1577 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.932244958575643 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -81.0226186746015 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.75766 5.75766 4.08165 create_atoms 2 region lower Created 1577 atoms create_atoms CPU = 0.000398159 secs group lower type 2 1577 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000 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*4.08165492862463 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.04082746431231 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 14 27 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 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 35 atoms, new total = 3119 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 14 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.02 | 18.02 | 18.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11132.001 0 -11132.001 -2174.1722 302 0 -11154.701 0 -11154.701 -7757.2173 Loop time of 20.495 on 1 procs for 302 steps with 3119 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 = -11132.0009931 -11154.7005791 -11154.7005791 Force two-norm initial, final = 10.0753 3.11916e-06 Force max component initial, final = 2.34517 8.62928e-07 Final line search alpha, max atom move = 1 8.62928e-07 Iterations, force evaluations = 302 570 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.253 | 20.253 | 20.253 | 0.0 | 98.82 Neigh | 0.10097 | 0.10097 | 0.10097 | 0.0 | 0.49 Comm | 0.098741 | 0.098741 | 0.098741 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04217 | | | 0.21 Nlocal: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 29459 ave 29459 max 29459 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: 1.32877e+06 ave 1.32877e+06 max 1.32877e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1328774 Ave neighs/atom = 426.026 Neighbor list builds = 4 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) = 18.02 | 18.02 | 18.02 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -11154.701 0 -11154.701 -7757.2173 53586.693 1302 0 -11155.403 0 -11155.403 -1915.7839 53251.602 Loop time of 74.3941 on 1 procs for 1000 steps with 3119 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -11154.7005791 -11155.4034881 -11155.4034881 Force two-norm initial, final = 306.887 0.031341 Force max component initial, final = 232.522 0.0303336 Final line search alpha, max atom move = 0.213131 0.00646505 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 73.118 | 73.118 | 73.118 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.30404 | 0.30404 | 0.30404 | 0.0 | 0.41 Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.9724 | | | 1.31 Nlocal: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 29494 ave 29494 max 29494 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: 1.32954e+06 ave 1.32954e+06 max 1.32954e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1329542 Ave neighs/atom = 426.272 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 2.2204e-16 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 14 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 16.91 | 16.91 | 16.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11155.403 0 -11155.403 -1915.7839 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3119 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: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 29515 ave 29515 max 29515 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: 1.33062e+06 ave 1.33062e+06 max 1.33062e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1330618 Ave neighs/atom = 426.617 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) = 16.91 | 16.91 | 16.91 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 -11155.403 -11155.403 80.874179 162.04524 4.0633714 -1915.7839 -1915.7839 -0.029936566 -5746.4132 -0.90855679 2.5885829 364.88824 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3119 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: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 29515 ave 29515 max 29515 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 665309 ave 665309 max 665309 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.33062e+06 ave 1.33062e+06 max 1.33062e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1330618 Ave neighs/atom = 426.617 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.8288/numatoms.out 3119 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11155.4034880944-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11155.4034880944-3119*${isolated_atom_energy} variable adjusted_pe_metal equal -11155.4034880944-3119*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -11155.4034880944 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.58858290912378 Angstroms write_dump all cfg output/dump_081.8288/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_081.8288/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:35