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 3.9946083426475534*${_u_distance} variable lattice_constant_converted equal 3.9946083426475534*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.9083418250084*${_u_distance} variable xmax_converted equal 67.9083418250084*1 variable ymin_converted equal -67.91233643335106*${_u_distance} variable ymin_converted equal -67.91233643335106*1 variable ymax_converted equal 67.91233643335106*${_u_distance} variable ymax_converted equal 67.91233643335106*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946083426475534*${_u_distance} variable zmax_converted equal 3.9946083426475534*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99460834264755 Lattice spacing in x,y,z = 3.99461 3.99461 3.99461 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 67.9083418250084 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.9083418250084 -67.9123364333511 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.9083418250084 -67.9123364333511 67.9123364333511 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.9083418250084 -67.9123364333511 67.9123364333511 0 ${zmax_converted} units box region whole block 0 67.9083418250084 -67.9123364333511 67.9123364333511 0 3.99460834264755 units box create_box 2 whole Created orthogonal box = (0 -67.9123 0) to (67.9083 67.9123 3.99461) 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 67.9123364333511 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 lattice fcc 3.99460834264755 orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.40447 5.40447 3.99461 create_atoms 1 region upper Created 1157 atoms create_atoms CPU = 0.000295877 secs group upper type 1 1157 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.65 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -67.9123364333511 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 lattice fcc 3.99460834264755 orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.40447 5.40447 3.99461 create_atoms 2 region lower Created 1157 atoms create_atoms CPU = 0.000192165 secs group lower type 2 1157 atoms in group lower displace_atoms lower move -7.65 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001 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*3.99460834264755 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730417132377 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 18 36 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 7.6001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2283 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 18 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.054 | 6.054 | 6.054 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7457.8154 0 -7457.8154 681.93237 168 0 -7480.3774 0 -7480.3774 -3269.9933 Loop time of 5.10662 on 1 procs for 168 steps with 2283 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -7457.81537753 -7480.37741223 -7480.37741223 Force two-norm initial, final = 18.7178 0.00592376 Force max component initial, final = 3.28722 0.0013551 Final line search alpha, max atom move = 0.000244141 3.30836e-07 Iterations, force evaluations = 168 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0419 | 5.0419 | 5.0419 | 0.0 | 98.73 Neigh | 0.023845 | 0.023845 | 0.023845 | 0.0 | 0.47 Comm | 0.025074 | 0.025074 | 0.025074 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01582 | | | 0.31 Nlocal: 2283 ave 2283 max 2283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13232 ave 13232 max 13232 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: 299198 ave 299198 max 299198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299198 Ave neighs/atom = 131.055 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) = 6.054 | 6.054 | 6.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 168 0 -7480.3774 0 -7480.3774 -3269.9933 36844.783 178 0 -7480.5218 0 -7480.5218 -1270.9965 36657.894 Loop time of 0.779775 on 1 procs for 10 steps with 2283 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -7480.37741223 -7480.52181375 -7480.52181375 Force two-norm initial, final = 72.6479 0.337065 Force max component initial, final = 58.1492 0.323665 Final line search alpha, max atom move = 9.35538e-08 3.02801e-08 Iterations, force evaluations = 10 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7648 | 0.7648 | 0.7648 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003319 | 0.003319 | 0.003319 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01166 | | | 1.49 Nlocal: 2283 ave 2283 max 2283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13237 ave 13237 max 13237 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: 299942 ave 299942 max 299942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299942 Ave neighs/atom = 131.381 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 -6.30324146298057e-20 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 18 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 6.192 | 6.192 | 6.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7480.5218 0 -7480.5218 -1270.9965 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2283 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: 2283 ave 2283 max 2283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13237 ave 13237 max 13237 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: 300254 ave 300254 max 300254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300254 Ave neighs/atom = 131.517 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) = 6.192 | 6.192 | 6.192 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 -7480.5218 -7480.5218 67.871217 135.82467 3.9765204 -1270.9965 -1270.9965 14.138434 -3830.0691 2.9410929 2.5310964 1080.3265 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2283 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: 2283 ave 2283 max 2283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13237 ave 13237 max 13237 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150127 ave 150127 max 150127 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 300254 ave 300254 max 300254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300254 Ave neighs/atom = 131.517 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.1450/numatoms.out 2283 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7480.521813747-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7480.521813747-2283*${isolated_atom_energy} variable adjusted_pe_metal equal -7480.521813747-2283*-6.30324146298057e-20 print "${adjusted_pe_metal} eV" file output/dump_056.1450/energy.out -7480.521813747 eV print "${mindist_metal} Angstroms" file output/dump_056.1450/mindistance.out 2.53109637970738 Angstroms write_dump all cfg output/dump_056.1450/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_056.1450/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06