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 4.05000014603138*${_u_distance} variable lattice_constant_converted equal 4.05000014603138*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 68.96901726882672*${_u_distance} variable xmax_converted equal 68.96901726882672*1 variable ymin_converted equal -68.97306726897276*${_u_distance} variable ymin_converted equal -68.97306726897276*1 variable ymax_converted equal 68.97306726897276*${_u_distance} variable ymax_converted equal 68.97306726897276*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.05000014603138*${_u_distance} variable zmax_converted equal 4.05000014603138*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000014603138 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 68.9690172688267 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9690172688267 -68.9730672689728 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9690172688267 -68.9730672689728 68.9730672689728 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9690172688267 -68.9730672689728 68.9730672689728 0 ${zmax_converted} units box region whole block 0 68.9690172688267 -68.9730672689728 68.9730672689728 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -68.9731 0) to (68.969 68.9731 4.05) 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 68.9730672689728 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70778 5.70778 4.05 create_atoms 1 region upper Created 1162 atoms create_atoms CPU = 0.000427961 secs group upper type 1 1162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.663223864666881 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.9730672689728 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70778 5.70778 4.05 create_atoms 2 region lower Created 1162 atoms create_atoms CPU = 0.000319958 secs group lower type 2 1162 atoms in group lower displace_atoms lower move -7.663223864666881 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_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*4.05000014603138 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500007301569 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2292 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.084 | 6.084 | 6.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7663.9239 0 -7663.9239 -1800.4774 366 0 -7684.5037 0 -7684.5037 -6877.5077 Loop time of 6.08703 on 1 procs for 366 steps with 2292 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 = -7663.92393532 -7684.50366226 -7684.50366226 Force two-norm initial, final = 13.0281 4.19087e-07 Force max component initial, final = 2.31554 9.70284e-08 Final line search alpha, max atom move = 1 9.70284e-08 Iterations, force evaluations = 366 723 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9923 | 5.9923 | 5.9923 | 0.0 | 98.44 Neigh | 0.0062718 | 0.0062718 | 0.0062718 | 0.0 | 0.10 Comm | 0.054428 | 0.054428 | 0.054428 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03399 | | | 0.56 Nlocal: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13693 ave 13693 max 13693 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: 323324 ave 323324 max 323324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323324 Ave neighs/atom = 141.066 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) = 6.085 | 6.085 | 6.085 Mbytes Step Temp E_pair E_mol TotEng Press Volume 366 0 -7684.5037 0 -7684.5037 -6877.5077 38531.739 1366 0 -7684.9784 0 -7684.9784 -1672.5001 38274.867 Loop time of 16.9006 on 1 procs for 1000 steps with 2292 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 = -7684.50366226 -7684.97837368 -7684.97837369 Force two-norm initial, final = 200.485 0.0214965 Force max component initial, final = 142.167 0.0185049 Final line search alpha, max atom move = 0.141089 0.00261083 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.263 | 16.263 | 16.263 | 0.0 | 96.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13928 | 0.13928 | 0.13928 | 0.0 | 0.82 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4981 | | | 2.95 Nlocal: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13728 ave 13728 max 13728 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: 322648 ave 322648 max 322648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322648 Ave neighs/atom = 140.771 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 6.223 | 6.223 | 6.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7684.9784 0 -7684.9784 -1672.5001 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2292 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: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13728 ave 13728 max 13728 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: 323368 ave 323368 max 323368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323368 Ave neighs/atom = 141.086 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) = 6.223 | 6.223 | 6.223 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 -7684.9784 -7684.9784 68.751338 137.94613 4.0357383 -1672.5001 -1672.5001 0.25536017 -5018.5276 0.77188243 2.5160481 704.88454 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2292 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: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13728 ave 13728 max 13728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 161684 ave 161684 max 161684 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 323368 ave 323368 max 323368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323368 Ave neighs/atom = 141.086 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_080.4727/numatoms.out 2292 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7684.9783736909-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7684.9783736909-2292*${isolated_atom_energy} variable adjusted_pe_metal equal -7684.9783736909-2292*0 print "${adjusted_pe_metal} eV" file output/dump_080.4727/energy.out -7684.9783736909 eV print "${mindist_metal} Angstroms" file output/dump_080.4727/mindistance.out 2.51604812010449 Angstroms write_dump all cfg output/dump_080.4727/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_080.4727/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:23