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 4.050004702806472*${_u_distance} variable lattice_constant_converted equal 4.050004702806472*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 66.4250159725308*${_u_distance} variable xmax_converted equal 66.4250159725308*1 variable ymin_converted equal -66.4290659772336*${_u_distance} variable ymin_converted equal -66.4290659772336*1 variable ymax_converted equal 66.4290659772336*${_u_distance} variable ymax_converted equal 66.4290659772336*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050004702806472*${_u_distance} variable zmax_converted equal 4.050004702806472*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000470280647 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 66.4250159725308 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4250159725308 -66.4290659772336 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4250159725308 -66.4290659772336 66.4290659772336 ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4250159725308 -66.4290659772336 66.4290659772336 0 ${zmax_converted} units box region whole block 0 66.4250159725308 -66.4290659772336 66.4290659772336 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -66.4291 0) to (66.425 66.4291 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 66.4290659772336 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67946 5.67946 4.05 create_atoms 1 region upper Created 1078 atoms create_atoms CPU = 0.000484228 secs group upper type 1 1078 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.380548760085527 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -66.4290659772336 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67946 5.67946 4.05 create_atoms 2 region lower Created 1078 atoms create_atoms CPU = 0.000331879 secs group lower type 2 1078 atoms in group lower displace_atoms lower move -7.380548760085527 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_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*4.05000470280647 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500235140324 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2128 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 17 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.046 | 6.046 | 6.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7105.7562 0 -7105.7562 -1226.0566 540 0 -7136.2902 0 -7136.2902 -6803.8324 Loop time of 6.76442 on 1 procs for 540 steps with 2128 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 = -7105.75616008 -7136.290198 -7136.290198 Force two-norm initial, final = 16.9259 1.14123e-05 Force max component initial, final = 3.36782 2.06381e-06 Final line search alpha, max atom move = 1 2.06381e-06 Iterations, force evaluations = 540 1034 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.573 | 6.573 | 6.573 | 0.0 | 97.17 Neigh | 0.061175 | 0.061175 | 0.061175 | 0.0 | 0.90 Comm | 0.083165 | 0.083165 | 0.083165 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0471 | | | 0.70 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14004 ave 14004 max 14004 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: 296884 ave 296884 max 296884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296884 Ave neighs/atom = 139.513 Neighbor list builds = 9 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) = 9.559 | 9.559 | 9.559 Mbytes Step Temp E_pair E_mol TotEng Press Volume 540 0 -7136.2902 0 -7136.2902 -6803.8324 35741.711 1540 0 -7136.7304 0 -7136.7304 -1597.4391 35503.753 Loop time of 13.1932 on 1 procs for 1000 steps with 2128 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 = -7136.290198 -7136.73040943 -7136.73040957 Force two-norm initial, final = 185.968 0.0218673 Force max component initial, final = 133.384 0.0218455 Final line search alpha, max atom move = 1 0.0218455 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.535 | 12.535 | 12.535 | 0.0 | 95.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1485 | 0.1485 | 0.1485 | 0.0 | 1.13 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5096 | | | 3.86 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14284 ave 14284 max 14284 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: 296876 ave 296876 max 296876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296876 Ave neighs/atom = 139.509 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 1.04222210722815e-10 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 16 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 9.321 | 9.321 | 9.321 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7136.7304 0 -7136.7304 -1597.4391 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14301 ave 14301 max 14301 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: 297004 ave 297004 max 297004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297004 Ave neighs/atom = 139.57 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) = 9.321 | 9.321 | 9.321 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 -7136.7304 -7136.7304 66.221777 132.85813 4.0353879 -1597.4391 -1597.4391 -0.03320579 -4793.2663 0.98226214 2.5760792 608.51028 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14301 ave 14301 max 14301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148502 ave 148502 max 148502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 297004 ave 297004 max 297004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297004 Ave neighs/atom = 139.57 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.1372/numatoms.out 2128 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7136.73040957475-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7136.73040957475-2128*${isolated_atom_energy} variable adjusted_pe_metal equal -7136.73040957475-2128*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_075.1372/energy.out -7136.73040979654 eV print "${mindist_metal} Angstroms" file output/dump_075.1372/mindistance.out 2.57607920767389 Angstroms write_dump all cfg output/dump_075.1372/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_075.1372/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:20