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 4.081654928624631*${_u_distance} variable lattice_constant_converted equal 4.081654928624631*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 53.21826925579387*${_u_distance} variable xmax_converted equal 53.21826925579387*1 variable ymin_converted equal -53.2223509107225*${_u_distance} variable ymin_converted equal -53.2223509107225*1 variable ymax_converted equal 53.2223509107225*${_u_distance} variable ymax_converted equal 53.2223509107225*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.081654928624631*${_u_distance} variable zmax_converted equal 4.081654928624631*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.08165492862463 Lattice spacing in x,y,z = 4.08165 4.08165 4.08165 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 53.2182692557939 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.2182692557939 -53.2223509107225 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.2182692557939 -53.2223509107225 53.2223509107225 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.2182692557939 -53.2223509107225 53.2223509107225 0 ${zmax_converted} units box region whole block 0 53.2182692557939 -53.2223509107225 53.2223509107225 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -53.2224 0) to (53.2183 53.2224 4.08165) 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 53.2223509107225 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.38268 4.38268 4.08165 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000273943 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.867282164682384 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.2223509107225 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.38268 4.38268 4.08165 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000185013 secs group lower type 2 682 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000 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*4.08165492862463 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.04082746431231 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 9 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 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1340 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.62 | 10.62 | 10.62 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4777.3575 0 -4777.3575 -2698.9428 468 0 -4787.8192 0 -4787.8192 -9358.3229 Loop time of 14.9805 on 1 procs for 468 steps with 1340 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4777.35754331 -4787.8192448 -4787.8192448 Force two-norm initial, final = 8.2036 1.2496e-05 Force max component initial, final = 1.80628 1.64145e-06 Final line search alpha, max atom move = 1 1.64145e-06 Iterations, force evaluations = 468 927 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.859 | 14.859 | 14.859 | 0.0 | 99.19 Neigh | 0.008738 | 0.008738 | 0.008738 | 0.0 | 0.06 Comm | 0.080044 | 0.080044 | 0.080044 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03229 | | | 0.22 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15402 ave 15402 max 15402 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: 569296 ave 569296 max 569296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569296 Ave neighs/atom = 424.848 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) = 10.62 | 10.62 | 10.62 Mbytes Step Temp E_pair E_mol TotEng Press Volume 468 0 -4787.8192 0 -4787.8192 -9358.3229 23121.77 1468 0 -4788.2716 0 -4788.2716 -2205.0539 22937.499 Loop time of 33.0351 on 1 procs for 1000 steps with 1340 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 = -4787.8192448 -4788.27158699 -4788.271587 Force two-norm initial, final = 159.231 0.00951818 Force max component initial, final = 113.075 0.00772329 Final line search alpha, max atom move = 0.135139 0.00104372 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.4 | 32.4 | 32.4 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15812 | 0.15812 | 0.15812 | 0.0 | 0.48 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4771 | | | 1.44 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15358 ave 15358 max 15358 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: 568920 ave 568920 max 568920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568920 Ave neighs/atom = 424.567 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 2.2204e-16 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 10.13 | 10.13 | 10.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4788.2716 0 -4788.2716 -2205.0539 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1340 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 | | 1.907e-06 | | |100.00 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15396 ave 15396 max 15396 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: 570384 ave 570384 max 570384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 570384 Ave neighs/atom = 425.66 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) = 10.13 | 10.13 | 10.13 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 -4788.2716 -4788.2716 53.001953 106.4447 4.0656515 -2205.0539 -2205.0539 0.5372765 -6615.5572 -0.14171366 2.6012332 215.40689 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15396 ave 15396 max 15396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 285192 ave 285192 max 285192 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 570384 ave 570384 max 570384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 570384 Ave neighs/atom = 425.66 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.7974/numatoms.out 1340 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4788.27158699746-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4788.27158699746-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -4788.27158699746-1340*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4788.27158699746 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.60123315754017 Angstroms write_dump all cfg output/dump_008.7974/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_008.7974/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:48