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 74.30401032688414*${_u_distance} variable xmax_converted equal 74.30401032688414*1 variable ymin_converted equal -74.30800493522679*${_u_distance} variable ymin_converted equal -74.30800493522679*1 variable ymax_converted equal 74.30800493522679*${_u_distance} variable ymax_converted equal 74.30800493522679*1 variable zmin_converted equal 0.0*${_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 74.3040103268841 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.3040103268841 -74.3080049352268 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.3040103268841 -74.3080049352268 74.3080049352268 ${zmin_converted} ${zmax_converted} units box region whole block 0 74.3040103268841 -74.3080049352268 74.3080049352268 0 ${zmax_converted} units box region whole block 0 74.3040103268841 -74.3080049352268 74.3080049352268 0 3.99460834264755 units box create_box 2 whole Created orthogonal box = (0 -74.308 0) to (74.304 74.308 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 74.3080049352268 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 lattice fcc 3.99460834264755 orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.58354 5.58354 3.99461 create_atoms 1 region upper Created 1386 atoms create_atoms CPU = 0.000337839 secs group upper type 1 1386 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.370483856982224 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.3080049352268 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 lattice fcc 3.99460834264755 orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.58354 5.58354 3.99461 create_atoms 2 region lower Created 1386 atoms create_atoms CPU = 0.000234127 secs group lower type 2 1386 atoms in group lower displace_atoms lower move -8.370483856982224 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 20 40 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 34 atoms, new total = 2738 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 = 20 40 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) = 10.05 | 10.05 | 10.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8953.1975 0 -8953.1975 384.99026 184 0 -8979.6991 0 -8979.6991 -3550.1115 Loop time of 6.61919 on 1 procs for 184 steps with 2738 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8953.19749957 -8979.6991231 -8979.6991231 Force two-norm initial, final = 17.5811 0.0129395 Force max component initial, final = 3.28177 0.00239302 Final line search alpha, max atom move = 6.10352e-05 1.46058e-07 Iterations, force evaluations = 184 373 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5413 | 6.5413 | 6.5413 | 0.0 | 98.82 Neigh | 0.024643 | 0.024643 | 0.024643 | 0.0 | 0.37 Comm | 0.032677 | 0.032677 | 0.032677 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02056 | | | 0.31 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15417 ave 15417 max 15417 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: 357584 ave 357584 max 357584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357584 Ave neighs/atom = 130.6 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) = 10.05 | 10.05 | 10.05 Mbytes Step Temp E_pair E_mol TotEng Press Volume 184 0 -8979.6991 0 -8979.6991 -3550.1115 44111.523 216 0 -8979.8631 0 -8979.8631 -1591.3677 43891.769 Loop time of 1.75741 on 1 procs for 32 steps with 2738 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8979.6991231 -8979.86311044 -8979.86311044 Force two-norm initial, final = 85.5424 0.370172 Force max component initial, final = 67.4546 0.364743 Final line search alpha, max atom move = 9.15257e-08 3.33834e-08 Iterations, force evaluations = 32 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7241 | 1.7241 | 1.7241 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.007216 | 0.007216 | 0.007216 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0261 | | | 1.49 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15427 ave 15427 max 15427 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: 359456 ave 359456 max 359456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 359456 Ave neighs/atom = 131.284 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 = 20 40 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) = 9.566 | 9.566 | 9.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8979.8631 0 -8979.8631 -1591.3677 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15427 ave 15427 max 15427 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: 360044 ave 360044 max 360044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360044 Ave neighs/atom = 131.499 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) = 9.566 | 9.566 | 9.566 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 -8979.8631 -8979.8631 74.259723 148.61601 3.9770785 -1591.3677 -1591.3677 -2.0084205 -4785.3505 13.255756 2.5221508 716.24919 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15427 ave 15427 max 15427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180022 ave 180022 max 180022 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 360044 ave 360044 max 360044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360044 Ave neighs/atom = 131.499 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.5077/numatoms.out 2738 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8979.86311044295-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8979.86311044295-2738*${isolated_atom_energy} variable adjusted_pe_metal equal -8979.86311044295-2738*-6.30324146298057e-20 print "${adjusted_pe_metal} eV" file output/dump_072.5077/energy.out -8979.86311044295 eV print "${mindist_metal} Angstroms" file output/dump_072.5077/mindistance.out 2.52215076253316 Angstroms write_dump all cfg output/dump_072.5077/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_072.5077/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08