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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.23375202370654*${_u_distance} variable xmax_converted equal 42.23375202370654*1 variable ymin_converted equal -42.23779728348772*${_u_distance} variable ymin_converted equal -42.23779728348772*1 variable ymax_converted equal 42.23779728348772*${_u_distance} variable ymax_converted equal 42.23779728348772*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 42.2337520237065 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2337520237065 -42.2377972834877 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2337520237065 -42.2377972834877 42.2377972834877 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.2337520237065 -42.2377972834877 42.2377972834877 0 ${zmax_converted} units box region whole block 0 42.2337520237065 -42.2377972834877 42.2377972834877 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -42.2378 0) to (42.2338 42.2378 4.04526) 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 42.2377972834877 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.03705 5.03705 4.04526 create_atoms 1 region upper Created 437 atoms create_atoms CPU = 0.000184059 secs group upper type 1 437 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.698137929009748 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.2377972834877 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.03705 5.03705 4.04526 create_atoms 2 region lower Created 437 atoms create_atoms CPU = 6.98566e-05 secs group lower type 2 437 atoms in group lower displace_atoms lower move -4.698137929009748 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 857 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 -2899.9003 0 -2899.9003 -1370.9542 253 0 -2910.561 0 -2910.561 -6655.5221 Loop time of 1.55422 on 1 procs for 253 steps with 857 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2899.90025799 -2910.5610058 -2910.5610058 Force two-norm initial, final = 14.9864 1.78289e-06 Force max component initial, final = 3.83918 4.30811e-07 Final line search alpha, max atom move = 1 4.30811e-07 Iterations, force evaluations = 253 487 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5184 | 1.5184 | 1.5184 | 0.0 | 97.69 Neigh | 0.00933 | 0.00933 | 0.00933 | 0.0 | 0.60 Comm | 0.016875 | 0.016875 | 0.016875 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009653 | | | 0.62 Nlocal: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6348 ave 6348 max 6348 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: 120522 ave 120522 max 120522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120522 Ave neighs/atom = 140.632 Neighbor list builds = 3 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 253 0 -2910.561 0 -2910.561 -6655.5221 14432.36 1253 0 -2910.7959 0 -2910.7959 -846.27347 14326.008 Loop time of 6.64404 on 1 procs for 1000 steps with 857 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 = -2910.5610058 -2910.79592202 -2910.79592203 Force two-norm initial, final = 83.5738 0.00577127 Force max component initial, final = 64.3346 0.00521496 Final line search alpha, max atom move = 0.080691 0.0004208 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3556 | 6.3556 | 6.3556 | 0.0 | 95.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06487 | 0.06487 | 0.06487 | 0.0 | 0.98 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2236 | | | 3.37 Nlocal: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6343 ave 6343 max 6343 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: 120364 ave 120364 max 120364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120364 Ave neighs/atom = 140.448 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2910.7959 0 -2910.7959 -846.27347 Loop time of 9.53674e-07 on 1 procs for 0 steps with 857 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: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6353 ave 6353 max 6353 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: 120892 ave 120892 max 120892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120892 Ave neighs/atom = 141.064 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) = 5.104 | 5.104 | 5.104 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 -2910.7959 -2910.7959 42.127498 84.475595 4.0255781 -846.27347 -846.27347 0.5817579 -2539.3211 -0.081056012 2.5343021 732.34857 Loop time of 9.53674e-07 on 1 procs for 0 steps with 857 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: 857 ave 857 max 857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6353 ave 6353 max 6353 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60446 ave 60446 max 60446 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120892 ave 120892 max 120892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120892 Ave neighs/atom = 141.064 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_033.3985/numatoms.out 857 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2910.79592202544-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2910.79592202544-857*${isolated_atom_energy} variable adjusted_pe_metal equal -2910.79592202544-857*0 print "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out -2910.79592202544 eV print "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out 2.53430210701381 Angstroms write_dump all cfg output/dump_033.3985/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_033.3985/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08