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 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 55.40855701410081*${_u_distance} variable xmax_converted equal 55.40855701410081*1 variable ymin_converted equal -55.4126307322314*${_u_distance} variable ymin_converted equal -55.4126307322314*1 variable ymax_converted equal 55.4126307322314*${_u_distance} variable ymax_converted equal 55.4126307322314*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 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 55.4085570141008 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.4085570141008 -55.4126307322314 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.4085570141008 -55.4126307322314 55.4126307322314 ${zmin_converted} ${zmax_converted} units box region whole block 0 55.4085570141008 -55.4126307322314 55.4126307322314 0 ${zmax_converted} units box region whole block 0 55.4085570141008 -55.4126307322314 55.4126307322314 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -55.4126 0) to (55.4086 55.4126 4.07372) 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 55.4126307322314 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -8 0 orient y 8 11 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 11 -8 0 orient y 8 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69061 5.69061 4.07372 create_atoms 1 region upper Created 742 atoms create_atoms CPU = 0.000328064 secs group upper type 1 742 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.1206617289309495 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -55.4126307322314 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 8 0 orient y -8 11 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 11 8 0 orient y -8 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69061 5.69061 4.07372 create_atoms 2 region lower Created 742 atoms create_atoms CPU = 0.000201941 secs group lower type 2 742 atoms in group lower displace_atoms lower move -6.1206617289309495 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 24 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1460 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4439.5521 0 -4439.5521 1798.6837 291 0 -4466.9768 0 -4466.9768 -4088.5666 Loop time of 4.89874 on 1 procs for 291 steps with 1460 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4439.55205413 -4466.9767859 -4466.9767859 Force two-norm initial, final = 31.4598 4.08187e-06 Force max component initial, final = 8.28148 9.27932e-07 Final line search alpha, max atom move = 1 9.27932e-07 Iterations, force evaluations = 291 562 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8222 | 4.8222 | 4.8222 | 0.0 | 98.44 Neigh | 0.021242 | 0.021242 | 0.021242 | 0.0 | 0.43 Comm | 0.037111 | 0.037111 | 0.037111 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01822 | | | 0.37 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11402 ave 11402 max 11402 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: 289020 ave 289020 max 289020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289020 Ave neighs/atom = 197.959 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) = 5.538 | 5.538 | 5.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 291 0 -4466.9768 0 -4466.9768 -4088.5666 25015.35 1291 0 -4467.1333 0 -4467.1333 -1334.2478 24873.059 Loop time of 17.1743 on 1 procs for 1000 steps with 1460 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 = -4466.9767859 -4467.1333223 -4467.13332242 Force two-norm initial, final = 72.6719 0.0464324 Force max component initial, final = 59.8062 0.035676 Final line search alpha, max atom move = 0.104426 0.00372549 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.696 | 16.696 | 16.696 | 0.0 | 97.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11349 | 0.11349 | 0.11349 | 0.0 | 0.66 Output | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3648 | | | 2.12 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11203 ave 11203 max 11203 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: 289304 ave 289304 max 289304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289304 Ave neighs/atom = 198.153 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 0.143095413925774 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.675 | 5.675 | 5.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4467.1333 0 -4467.1333 -1334.2478 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11264 ave 11264 max 11264 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: 289464 ave 289464 max 289464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289464 Ave neighs/atom = 198.263 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) = 5.675 | 5.675 | 5.675 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 -4467.1333 -4467.1333 55.1837 110.82526 4.0670509 -1334.2478 -1334.2478 -1.7337715 -3998.7155 -2.2942779 2.58677 615.30247 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1460 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 | | 1.192e-06 | | |100.00 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11264 ave 11264 max 11264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144732 ave 144732 max 144732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289464 ave 289464 max 289464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289464 Ave neighs/atom = 198.263 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.0547/numatoms.out 1460 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4467.13332242457-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4467.13332242457-1460*${isolated_atom_energy} variable adjusted_pe_metal equal -4467.13332242457-1460*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_072.0547/energy.out -4676.0526267562 eV print "${mindist_metal} Angstroms" file output/dump_072.0547/mindistance.out 2.58676998670229 Angstroms write_dump all cfg output/dump_072.0547/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_072.0547/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:22