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 4.032082897424699*${_u_distance} variable lattice_constant_converted equal 4.032082897424699*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 54.24612742858757*${_u_distance} variable xmax_converted equal 54.24612742858757*1 variable ymin_converted equal -54.250159511484995*${_u_distance} variable ymin_converted equal -54.250159511484995*1 variable ymax_converted equal 54.250159511484995*${_u_distance} variable ymax_converted equal 54.250159511484995*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082897424699*${_u_distance} variable zmax_converted equal 4.032082897424699*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0320828974247 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 54.2461274285876 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.2461274285876 -54.250159511485 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.2461274285876 -54.250159511485 54.250159511485 ${zmin_converted} ${zmax_converted} units box region whole block 0 54.2461274285876 -54.250159511485 54.250159511485 0 ${zmax_converted} units box region whole block 0 54.2461274285876 -54.250159511485 54.250159511485 0 4.0320828974247 units box create_box 2 whole Created orthogonal box = (0 -54.2502 0) to (54.2461 54.2502 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 54.250159511485 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69434 5.69434 4.03208 create_atoms 1 region upper Created 726 atoms create_atoms CPU = 0.000243902 secs group upper type 1 726 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.054130821183169 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -54.250159511485 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 9 0 orient y -9 10 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 10 9 0 orient y -9 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69434 5.69434 4.03208 create_atoms 2 region lower Created 726 atoms create_atoms CPU = 0.000134945 secs group lower type 2 726 atoms in group lower displace_atoms lower move -6.054130821183169 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002 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*4.0320828974247 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604144871235 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 = 15 29 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 28 atoms, new total = 1424 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 = 15 29 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) = 5.086 | 5.086 | 5.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4753.6802 0 -4753.6802 -1030.8563 222 0 -4772.3801 0 -4772.3801 -9758.3355 Loop time of 1.45164 on 1 procs for 222 steps with 1424 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 = -4753.68022832 -4772.38011681 -4772.38011681 Force two-norm initial, final = 17.6171 1.72401e-06 Force max component initial, final = 3.82991 2.53116e-07 Final line search alpha, max atom move = 1 2.53116e-07 Iterations, force evaluations = 222 427 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4158 | 1.4158 | 1.4158 | 0.0 | 97.53 Neigh | 0.0033131 | 0.0033131 | 0.0033131 | 0.0 | 0.23 Comm | 0.019614 | 0.019614 | 0.019614 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01296 | | | 0.89 Nlocal: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8795 ave 8795 max 8795 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: 150604 ave 150604 max 150604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150604 Ave neighs/atom = 105.761 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) = 5.086 | 5.086 | 5.086 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -4772.3801 0 -4772.3801 -9758.3355 23731.72 1222 0 -4772.8024 0 -4772.8024 -3544.01 23545.452 Loop time of 7.64782 on 1 procs for 1000 steps with 1424 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 = -4772.38011681 -4772.80243761 -4772.80243762 Force two-norm initial, final = 149.745 0.00922132 Force max component initial, final = 114.41 0.00598132 Final line search alpha, max atom move = 0.0666248 0.000398505 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2303 | 7.2303 | 7.2303 | 0.0 | 94.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.089752 | 0.089752 | 0.089752 | 0.0 | 1.17 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3278 | | | 4.29 Nlocal: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8734 ave 8734 max 8734 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: 150336 ave 150336 max 150336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150336 Ave neighs/atom = 105.573 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 = 15 29 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) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4772.8024 0 -4772.8024 -3544.01 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1424 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: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8771 ave 8771 max 8771 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: 160444 ave 160444 max 160444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160444 Ave neighs/atom = 112.671 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) = 5.223 | 5.223 | 5.223 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 -4772.8024 -4772.8024 54.002744 108.50032 4.018465 -3544.01 -3544.01 0.40517975 -10632.516 0.080447568 2.6261988 256.61142 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1424 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: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8771 ave 8771 max 8771 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80222 ave 80222 max 80222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160444 ave 160444 max 160444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160444 Ave neighs/atom = 112.671 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_083.9744/numatoms.out 1424 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4772.80243761645-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4772.80243761645-1424*${isolated_atom_energy} variable adjusted_pe_metal equal -4772.80243761645-1424*0 print "${adjusted_pe_metal} eV" file output/dump_083.9744/energy.out -4772.80243761645 eV print "${mindist_metal} Angstroms" file output/dump_083.9744/mindistance.out 2.626198785987 Angstroms write_dump all cfg output/dump_083.9744/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_083.9744/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09