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 4.128871455788613*${_u_distance} variable lattice_constant_converted equal 4.128871455788613*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 49.88934361935616*${_u_distance} variable xmax_converted equal 49.88934361935616*1 variable ymin_converted equal -49.89347249081195*${_u_distance} variable ymin_converted equal -49.89347249081195*1 variable ymax_converted equal 49.89347249081195*${_u_distance} variable ymax_converted equal 49.89347249081195*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.128871455788613*${_u_distance} variable zmax_converted equal 4.128871455788613*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.12887145578861 Lattice spacing in x,y,z = 4.12887 4.12887 4.12887 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 49.8893436193562 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 49.8893436193562 -49.893472490812 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 49.8893436193562 -49.893472490812 49.893472490812 ${zmin_converted} ${zmax_converted} units box region whole block 0 49.8893436193562 -49.893472490812 49.893472490812 0 ${zmax_converted} units box region whole block 0 49.8893436193562 -49.893472490812 49.893472490812 0 4.12887145578861 units box create_box 2 whole Created orthogonal box = (0 -49.8935 0) to (49.8893 49.8935 4.12887) 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 49.893472490812 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.46733 5.46733 4.12887 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000310183 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.437370688117558 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -49.893472490812 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.46733 5.46733 4.12887 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.000159025 secs group lower type 2 586 atoms in group lower displace_atoms lower move -5.437370688117558 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_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*4.12887145578861 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0644357278943 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 11 22 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1150 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4239.6415 0 -4239.6415 -8506.5042 401 0 -4256.7795 0 -4256.7795 -12500.962 Loop time of 6.8252 on 1 procs for 401 steps with 1150 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 = -4239.64149684 -4256.77949337 -4256.77949337 Force two-norm initial, final = 20.6677 9.65103e-06 Force max component initial, final = 4.56269 2.4116e-06 Final line search alpha, max atom move = 1 2.4116e-06 Iterations, force evaluations = 401 789 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7436 | 6.7436 | 6.7436 | 0.0 | 98.80 Neigh | 0.016164 | 0.016164 | 0.016164 | 0.0 | 0.24 Comm | 0.04333 | 0.04333 | 0.04333 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02207 | | | 0.32 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8908 ave 8908 max 8908 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: 206328 ave 206328 max 206328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206328 Ave neighs/atom = 179.416 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) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 401 0 -4256.7795 0 -4256.7795 -12500.962 20554.782 1401 0 -4257.6163 0 -4257.6163 -1463.8534 20332.052 Loop time of 16.9136 on 1 procs for 1000 steps with 1150 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 = -4256.77949337 -4257.61629496 -4257.61629496 Force two-norm initial, final = 214.74 0.000905296 Force max component initial, final = 157.777 0.000711591 Final line search alpha, max atom move = 1 0.000711591 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.496 | 16.496 | 16.496 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098018 | 0.098018 | 0.098018 | 0.0 | 0.58 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3198 | | | 1.89 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9069 ave 9069 max 9069 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: 206036 ave 206036 max 206036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206036 Ave neighs/atom = 179.162 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.58 | 5.58 | 5.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4257.6163 0 -4257.6163 -1463.8534 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1150 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: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9099 ave 9099 max 9099 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: 211728 ave 211728 max 211728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211728 Ave neighs/atom = 184.111 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) = 5.58 | 5.58 | 5.58 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 -4257.6163 -4257.6163 49.575383 99.786945 4.1099959 -1463.8534 -1463.8534 -0.055720893 -4391.4718 -0.032674269 2.5793695 886.73183 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1150 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: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9099 ave 9099 max 9099 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105864 ave 105864 max 105864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211728 ave 211728 max 211728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211728 Ave neighs/atom = 184.111 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_048.8879/numatoms.out 1150 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4257.61629496407-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4257.61629496407-1150*${isolated_atom_energy} variable adjusted_pe_metal equal -4257.61629496407-1150*0 print "${adjusted_pe_metal} eV" file output/dump_048.8879/energy.out -4257.61629496407 eV print "${mindist_metal} Angstroms" file output/dump_048.8879/mindistance.out 2.57936954348476 Angstroms write_dump all cfg output/dump_048.8879/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_048.8879/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:23