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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 28.459954590287893*${_u_distance} variable xmax_converted equal 28.459954590287893*1 variable ymin_converted equal -56.9239340259524*${_u_distance} variable ymin_converted equal -56.9239340259524*1 variable ymax_converted equal 56.9239340259524*${_u_distance} variable ymax_converted equal 56.9239340259524*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 28.4599545902879 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.4599545902879 -56.9239340259524 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 28.4599545902879 -56.9239340259524 56.9239340259524 ${zmin_converted} ${zmax_converted} units box region whole block 0 28.4599545902879 -56.9239340259524 56.9239340259524 0 ${zmax_converted} units box region whole block 0 28.4599545902879 -56.9239340259524 56.9239340259524 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -56.9239 0) to (28.46 56.9239 4.02485) 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 56.9239340259524 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 7 -1 0 orient y 1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.55359 4.55359 4.02485 create_atoms 1 region upper Created 402 atoms create_atoms CPU = 0.000174999 secs group upper type 1 402 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.181980515339464 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.9239340259524 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 7 1 0 orient y -1 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.55359 4.55359 4.02485 create_atoms 2 region lower Created 402 atoms create_atoms CPU = 6.48499e-05 secs group lower type 2 402 atoms in group lower displace_atoms lower move -3.181980515339464 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 28 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 792 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2081.9466 0 -2081.9466 -630.8188 273 0 -2089.2872 0 -2089.2872 -3139.8111 Loop time of 1.37771 on 1 procs for 273 steps with 792 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2081.94660953 -2089.28723095 -2089.28723095 Force two-norm initial, final = 12.3487 2.03492e-05 Force max component initial, final = 3.77199 3.32433e-06 Final line search alpha, max atom move = 1 3.32433e-06 Iterations, force evaluations = 273 544 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3494 | 1.3494 | 1.3494 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018529 | 0.018529 | 0.018529 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009804 | | | 0.71 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6413 ave 6413 max 6413 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: 110268 ave 110268 max 110268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110268 Ave neighs/atom = 139.227 Neighbor list builds = 0 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press Volume 273 0 -2089.2872 0 -2089.2872 -3139.8111 13040.922 1273 0 -2089.329 0 -2089.329 -430.81571 12995.576 Loop time of 6.02271 on 1 procs for 1000 steps with 792 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 = -2089.28723095 -2089.3290116 -2089.32901165 Force two-norm initial, final = 34.1636 0.0263531 Force max component initial, final = 24.9797 0.0208788 Final line search alpha, max atom move = 0.073583 0.00153632 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7247 | 5.7247 | 5.7247 | 0.0 | 95.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067197 | 0.067197 | 0.067197 | 0.0 | 1.12 Output | 1.3828e-05 | 1.3828e-05 | 1.3828e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2308 | | | 3.83 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6398 ave 6398 max 6398 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: 110796 ave 110796 max 110796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110796 Ave neighs/atom = 139.894 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.103 | 5.103 | 5.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2089.329 0 -2089.329 -430.81571 Loop time of 9.53674e-07 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6413 ave 6413 max 6413 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: 110796 ave 110796 max 110796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110796 Ave neighs/atom = 139.894 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) = 5.103 | 5.103 | 5.103 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 -2089.329 -2089.329 28.420521 113.84787 4.0164152 -430.81571 -430.81571 0.45100526 -1295.4668 2.5686744 2.515658 401.00924 Loop time of 9.53674e-07 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6413 ave 6413 max 6413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55398 ave 55398 max 55398 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110796 ave 110796 max 110796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110796 Ave neighs/atom = 139.894 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_016.2602/numatoms.out 792 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2089.32901165347-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2089.32901165347-792*${isolated_atom_energy} variable adjusted_pe_metal equal -2089.32901165347-792*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_016.2602/energy.out -2064.98747527419 eV print "${mindist_metal} Angstroms" file output/dump_016.2602/mindistance.out 2.51565796032687 Angstroms write_dump all cfg output/dump_016.2602/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_016.2602/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:07