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 60.14772739540446*${_u_distance} variable xmax_converted equal 60.14772739540446*1 variable ymin_converted equal -60.15180111353505*${_u_distance} variable ymin_converted equal -60.15180111353505*1 variable ymax_converted equal 60.15180111353505*${_u_distance} variable ymax_converted equal 60.15180111353505*1 variable zmin_converted equal 0.0*${_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 60.1477273954045 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1477273954045 -60.1518011135351 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1477273954045 -60.1518011135351 60.1518011135351 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1477273954045 -60.1518011135351 60.1518011135351 0 ${zmax_converted} units box region whole block 0 60.1477273954045 -60.1518011135351 60.1518011135351 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -60.1518 0) to (60.1477 60.1518 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 60.1518011135351 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.51814 5.51814 4.07372 create_atoms 1 region upper Created 874 atoms create_atoms CPU = 0.000365019 secs group upper type 1 874 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.64417037710503 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.1518011135351 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.51814 5.51814 4.07372 create_atoms 2 region lower Created 874 atoms create_atoms CPU = 0.000227928 secs group lower type 2 874 atoms in group lower displace_atoms lower move -6.64417037710503 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 13 26 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 26 atoms, new total = 1722 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 = 13 26 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5249.9859 0 -5249.9859 193.75438 293 0 -5268.2589 0 -5268.2589 -3283.3043 Loop time of 5.76489 on 1 procs for 293 steps with 1722 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 = -5249.98593569 -5268.25885617 -5268.25885617 Force two-norm initial, final = 21.4126 1.0271e-05 Force max component initial, final = 4.82065 1.32559e-06 Final line search alpha, max atom move = 1 1.32559e-06 Iterations, force evaluations = 293 576 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6933 | 5.6933 | 5.6933 | 0.0 | 98.76 Neigh | 0.0082619 | 0.0082619 | 0.0082619 | 0.0 | 0.14 Comm | 0.041989 | 0.041989 | 0.041989 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02139 | | | 0.37 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12576 ave 12576 max 12576 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: 340872 ave 340872 max 340872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340872 Ave neighs/atom = 197.951 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) = 5.992 | 5.992 | 5.992 Mbytes Step Temp E_pair E_mol TotEng Press Volume 293 0 -5268.2589 0 -5268.2589 -3283.3043 29477.377 1293 0 -5268.4037 0 -5268.4037 -765.75462 29322.306 Loop time of 20.2971 on 1 procs for 1000 steps with 1722 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 = -5268.25885617 -5268.40371604 -5268.40371604 Force two-norm initial, final = 76.1859 0.00781209 Force max component initial, final = 59.0567 0.0062057 Final line search alpha, max atom move = 1 0.0062057 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.705 | 19.705 | 19.705 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14248 | 0.14248 | 0.14248 | 0.0 | 0.70 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4493 | | | 2.21 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13854 ave 13854 max 13854 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: 341304 ave 341304 max 341304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341304 Ave neighs/atom = 198.202 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 = 13 26 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) = 6.13 | 6.13 | 6.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5268.4037 0 -5268.4037 -765.75462 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1722 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 | | 2.146e-06 | | |100.00 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13854 ave 13854 max 13854 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: 341412 ave 341412 max 341412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341412 Ave neighs/atom = 198.265 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) = 6.13 | 6.13 | 6.13 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 -5268.4037 -5268.4037 59.95653 120.3036 4.0652101 -765.75462 -765.75462 -0.22307026 -2296.7024 -0.33837238 2.5675728 1020.5527 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1722 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 | | 1.907e-06 | | |100.00 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13854 ave 13854 max 13854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170706 ave 170706 max 170706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 341412 ave 341412 max 341412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341412 Ave neighs/atom = 198.265 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.6015/numatoms.out 1722 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5268.40371604329-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5268.40371604329-1722*${isolated_atom_energy} variable adjusted_pe_metal equal -5268.40371604329-1722*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_056.6015/energy.out -5514.81401882347 eV print "${mindist_metal} Angstroms" file output/dump_056.6015/mindistance.out 2.56757281148667 Angstroms write_dump all cfg output/dump_056.6015/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_056.6015/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:26