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 4.032082897424699*${_u_distance} variable lattice_constant_converted equal 4.032082897424699*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 45.9728183160617*${_u_distance} variable xmax_converted equal 45.9728183160617*1 variable ymin_converted equal -45.97685039895912*${_u_distance} variable ymin_converted equal -45.97685039895912*1 variable ymax_converted equal 45.97685039895912*${_u_distance} variable ymax_converted equal 45.97685039895912*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082897424699*${_u_distance} variable zmax_converted equal 4.032082897424699*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0320828974247 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 45.9728183160617 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9728183160617 -45.9768503989591 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9728183160617 -45.9768503989591 45.9768503989591 ${zmin_converted} ${zmax_converted} units box region whole block 0 45.9728183160617 -45.9768503989591 45.9768503989591 0 ${zmax_converted} units box region whole block 0 45.9728183160617 -45.9768503989591 45.9768503989591 0 4.0320828974247 units box create_box 2 whole Created orthogonal box = (0 -45.9769 0) to (45.9728 45.9769 4.03208) 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 45.9768503989591 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -3 0 orient y 3 11 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 11 -3 0 orient y 3 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95092 4.95092 4.03208 create_atoms 1 region upper Created 522 atoms create_atoms CPU = 0.000271082 secs group upper type 1 522 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.13078941294612 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.9768503989591 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 3 0 orient y -3 11 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 11 3 0 orient y -3 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95092 4.95092 4.03208 create_atoms 2 region lower Created 522 atoms create_atoms CPU = 0.000121117 secs group lower type 2 522 atoms in group lower displace_atoms lower move -5.13078941294612 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002 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*4.0320828974247 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604144871235 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 25 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1026 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3412.0971 0 -3412.0971 3298.5097 206 0 -3433.6819 0 -3433.6819 -4816.2056 Loop time of 0.983294 on 1 procs for 206 steps with 1026 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3412.09713614 -3433.6819468 -3433.6819468 Force two-norm initial, final = 28.357 2.45966e-05 Force max component initial, final = 5.75068 5.85582e-06 Final line search alpha, max atom move = 1 5.85582e-06 Iterations, force evaluations = 206 407 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95819 | 0.95819 | 0.95819 | 0.0 | 97.45 Neigh | 0.002284 | 0.002284 | 0.002284 | 0.0 | 0.23 Comm | 0.014261 | 0.014261 | 0.014261 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008561 | | | 0.87 Nlocal: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6899 ave 6899 max 6899 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: 113788 ave 113788 max 113788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113788 Ave neighs/atom = 110.904 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) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press Volume 206 0 -3433.6819 0 -3433.6819 -4816.2056 17045.109 1206 0 -3433.7584 0 -3433.7584 -1701.2005 16977.878 Loop time of 5.5519 on 1 procs for 1000 steps with 1026 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3433.6819468 -3433.75839183 -3433.75839183 Force two-norm initial, final = 52.7781 0.00127602 Force max component initial, final = 40.9688 0.00104522 Final line search alpha, max atom move = 0.301148 0.000314767 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2338 | 5.2338 | 5.2338 | 0.0 | 94.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.070425 | 0.070425 | 0.070425 | 0.0 | 1.27 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2477 | | | 4.46 Nlocal: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6899 ave 6899 max 6899 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: 114248 ave 114248 max 114248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114248 Ave neighs/atom = 111.353 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.7584 0 -3433.7584 -1701.2005 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1026 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: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6899 ave 6899 max 6899 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: 119688 ave 119688 max 119688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119688 Ave neighs/atom = 116.655 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) = 5.133 | 5.133 | 5.133 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 -3433.7584 -3433.7584 45.918663 91.953701 4.0209157 -1701.2005 -1701.2005 0.098520079 -5103.6869 -0.013069526 2.5128609 829.01264 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1026 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: 1026 ave 1026 max 1026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6899 ave 6899 max 6899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59844 ave 59844 max 59844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119688 ave 119688 max 119688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119688 Ave neighs/atom = 116.655 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_030.5102/numatoms.out 1026 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3433.75839182877-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3433.75839182877-1026*${isolated_atom_energy} variable adjusted_pe_metal equal -3433.75839182877-1026*0 print "${adjusted_pe_metal} eV" file output/dump_030.5102/energy.out -3433.75839182877 eV print "${mindist_metal} Angstroms" file output/dump_030.5102/mindistance.out 2.51286088482594 Angstroms write_dump all cfg output/dump_030.5102/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_030.5102/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06