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 20.36859065294266*${_u_distance} variable xmax_converted equal 20.36859065294266*1 variable ymin_converted equal -40.74125502401591*${_u_distance} variable ymin_converted equal -40.74125502401591*1 variable ymax_converted equal 40.74125502401591*${_u_distance} variable ymax_converted equal 40.74125502401591*1 variable zmin_converted equal 0.0*${_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 20.3685906529427 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.3685906529427 -40.7412550240159 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.3685906529427 -40.7412550240159 40.7412550240159 ${zmin_converted} ${zmax_converted} units box region whole block 0 20.3685906529427 -40.7412550240159 40.7412550240159 0 ${zmax_converted} units box region whole block 0 20.3685906529427 -40.7412550240159 40.7412550240159 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -40.7413 0) to (20.3686 40.7413 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 40.7412550240159 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70321 5.70321 4.07372 create_atoms 1 region upper Created 202 atoms create_atoms CPU = 0.000160933 secs group upper type 1 202 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.25 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.7412550240159 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70321 5.70321 4.07372 create_atoms 2 region lower Created 202 atoms create_atoms CPU = 5.22137e-05 secs group lower type 2 202 atoms in group lower displace_atoms lower move -2.25 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 5 18 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 12 atoms, new total = 392 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 = 5 18 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) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1188.7954 0 -1188.7954 1561.7159 195 0 -1198.5773 0 -1198.5773 -6837.1 Loop time of 0.926154 on 1 procs for 195 steps with 392 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1188.79544766 -1198.57728647 -1198.57728647 Force two-norm initial, final = 15.1045 1.15954e-05 Force max component initial, final = 4.67378 1.70804e-06 Final line search alpha, max atom move = 1 1.70804e-06 Iterations, force evaluations = 195 381 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90769 | 0.90769 | 0.90769 | 0.0 | 98.01 Neigh | 0.0026948 | 0.0026948 | 0.0026948 | 0.0 | 0.29 Comm | 0.010943 | 0.010943 | 0.010943 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004822 | | | 0.52 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4887 ave 4887 max 4887 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: 77164 ave 77164 max 77164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77164 Ave neighs/atom = 196.847 Neighbor list builds = 2 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) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press Volume 195 0 -1198.5773 0 -1198.5773 -6837.1 6761.0844 1195 0 -1198.6919 0 -1198.6919 -2187.0723 6695.7307 Loop time of 4.90145 on 1 procs for 1000 steps with 392 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1198.57728647 -1198.6919247 -1198.6919247 Force two-norm initial, final = 32.5947 0.000391236 Force max component initial, final = 25.4806 0.000300947 Final line search alpha, max atom move = 1 0.000300947 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6836 | 4.6836 | 4.6836 | 0.0 | 95.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.054833 | 0.054833 | 0.054833 | 0.0 | 1.12 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.163 | | | 3.32 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176 ave 5176 max 5176 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: 77288 ave 77288 max 77288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77288 Ave neighs/atom = 197.163 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 = 5 18 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1198.6919 0 -1198.6919 -2187.0723 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176 ave 5176 max 5176 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: 77432 ave 77432 max 77432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77432 Ave neighs/atom = 197.531 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) = 4.625 | 4.625 | 4.625 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 -1198.6919 -1198.6919 20.251629 81.48251 4.0576409 -2187.0723 -2187.0723 0.071597977 -6561.3285 0.039894852 2.5943637 208.43338 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176 ave 5176 max 5176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38716 ave 38716 max 38716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77432 ave 77432 max 77432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77432 Ave neighs/atom = 197.531 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_073.7398/numatoms.out 392 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1198.69192469796-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1198.69192469796-392*${isolated_atom_energy} variable adjusted_pe_metal equal -1198.69192469796-392*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_073.7398/energy.out -1254.78532695686 eV print "${mindist_metal} Angstroms" file output/dump_073.7398/mindistance.out 2.59436371733143 Angstroms write_dump all cfg output/dump_073.7398/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_073.7398/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05