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 4.031036108732224*${_u_distance} variable lattice_constant_converted equal 4.031036108732224*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 21.70779378903319*${_u_distance} variable xmax_converted equal 21.70779378903319*1 variable ymin_converted equal -43.419618614175114*${_u_distance} variable ymin_converted equal -43.419618614175114*1 variable ymax_converted equal 43.419618614175114*${_u_distance} variable ymax_converted equal 43.419618614175114*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031036108732224*${_u_distance} variable zmax_converted equal 4.031036108732224*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03103610873222 Lattice spacing in x,y,z = 4.03104 4.03104 4.03104 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 21.7077937890332 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.7077937890332 -43.4196186141751 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.7077937890332 -43.4196186141751 43.4196186141751 ${zmin_converted} ${zmax_converted} units box region whole block 0 21.7077937890332 -43.4196186141751 43.4196186141751 0 ${zmax_converted} units box region whole block 0 21.7077937890332 -43.4196186141751 43.4196186141751 0 4.03103610873222 units box create_box 2 whole Created orthogonal box = (0 -43.4196 0) to (21.7078 43.4196 4.03104) 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 43.4196186141751 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23981 5.23981 4.03104 create_atoms 1 region upper Created 233 atoms create_atoms CPU = 0.000211954 secs group upper type 1 233 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.4233241632105265 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -43.4196186141751 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23981 5.23981 4.03104 create_atoms 2 region lower Created 233 atoms create_atoms CPU = 8.39233e-05 secs group lower type 2 233 atoms in group lower displace_atoms lower move -2.4233241632105265 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_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*4.03103610873222 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01551805436611 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 6 23 2 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 458 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1518.5674 0 -1518.5674 5315.2305 225 0 -1532.4582 0 -1532.4582 -3363.906 Loop time of 0.597792 on 1 procs for 225 steps with 458 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1518.56739792 -1532.45821284 -1532.45821284 Force two-norm initial, final = 23.7906 4.84522e-06 Force max component initial, final = 7.45049 1.73581e-06 Final line search alpha, max atom move = 1 1.73581e-06 Iterations, force evaluations = 225 444 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58041 | 0.58041 | 0.58041 | 0.0 | 97.09 Neigh | 0.0015571 | 0.0015571 | 0.0015571 | 0.0 | 0.26 Comm | 0.010331 | 0.010331 | 0.010331 | 0.0 | 1.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005489 | | | 0.92 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4137 ave 4137 max 4137 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: 59352 ave 59352 max 59352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59352 Ave neighs/atom = 129.59 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) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 225 0 -1532.4582 0 -1532.4582 -3363.906 7598.8588 1225 0 -1532.4939 0 -1532.4939 -295.23313 7566.8298 Loop time of 2.60871 on 1 procs for 1000 steps with 458 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1532.45821284 -1532.49392353 -1532.49392353 Force two-norm initial, final = 23.311 0.00101639 Force max component initial, final = 18.0813 0.00084968 Final line search alpha, max atom move = 1 0.00084968 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4258 | 2.4258 | 2.4258 | 0.0 | 92.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04249 | 0.04249 | 0.04249 | 0.0 | 1.63 Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1404 | | | 5.38 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4127 ave 4127 max 4127 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: 59700 ave 59700 max 59700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59700 Ave neighs/atom = 130.349 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 4.607 | 4.607 | 4.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1532.4939 0 -1532.4939 -295.23313 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4132 ave 4132 max 4132 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: 59724 ave 59724 max 59724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59724 Ave neighs/atom = 130.402 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) = 4.607 | 4.607 | 4.607 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 -1532.4939 -1532.4939 21.648187 86.839237 4.0250977 -295.23313 -295.23313 -0.1121506 -885.40759 -0.17964361 2.4987606 437.54945 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4132 ave 4132 max 4132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29862 ave 29862 max 29862 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59724 ave 59724 max 59724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59724 Ave neighs/atom = 130.402 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_043.6028/numatoms.out 458 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1532.49392353213-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1532.49392353213-458*${isolated_atom_energy} variable adjusted_pe_metal equal -1532.49392353213-458*0 print "${adjusted_pe_metal} eV" file output/dump_043.6028/energy.out -1532.49392353213 eV print "${mindist_metal} Angstroms" file output/dump_043.6028/mindistance.out 2.49876061965526 Angstroms write_dump all cfg output/dump_043.6028/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_043.6028/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03