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 4.045270472764969*${_u_distance} variable lattice_constant_converted equal 4.045270472764969*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.13726894962166*${_u_distance} variable xmax_converted equal 60.13726894962166*1 variable ymin_converted equal -60.14131422009442*${_u_distance} variable ymin_converted equal -60.14131422009442*1 variable ymax_converted equal 60.14131422009442*${_u_distance} variable ymax_converted equal 60.14131422009442*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045270472764969*${_u_distance} variable zmax_converted equal 4.045270472764969*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04527047276497 Lattice spacing in x,y,z = 4.04527 4.04527 4.04527 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 60.1372689496217 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1372689496217 -60.1413142200944 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1372689496217 -60.1413142200944 60.1413142200944 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.1372689496217 -60.1413142200944 60.1413142200944 0 ${zmax_converted} units box region whole block 0 60.1372689496217 -60.1413142200944 60.1413142200944 0 4.04527047276497 units box create_box 2 whole Created orthogonal box = (0 -60.1413 0) to (60.1373 60.1413 4.04527) 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 60.1413142200944 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -10 0 orient y 10 11 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 11 -10 0 orient y 10 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.7144 5.7144 4.04527 create_atoms 1 region upper Created 885 atoms create_atoms CPU = 0.000283003 secs group upper type 1 885 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.1413142200944 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 10 0 orient y -10 11 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 11 10 0 orient y -10 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.7144 5.7144 4.04527 create_atoms 2 region lower Created 885 atoms create_atoms CPU = 0.000159025 secs group lower type 2 885 atoms in group lower displace_atoms lower move -6.689730936293327 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_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*4.04527047276497 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02263523638248 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 13 26 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1744 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5917.4852 0 -5917.4852 -1515.7414 290 0 -5937.0415 0 -5937.0415 -7156.5039 Loop time of 4.74749 on 1 procs for 290 steps with 1744 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5917.48518148 -5937.04147205 -5937.04147205 Force two-norm initial, final = 15.9576 3.55958e-06 Force max component initial, final = 3.21709 5.78693e-07 Final line search alpha, max atom move = 1 5.78693e-07 Iterations, force evaluations = 290 555 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6552 | 4.6552 | 4.6552 | 0.0 | 98.06 Neigh | 0.02315 | 0.02315 | 0.02315 | 0.0 | 0.49 Comm | 0.04623 | 0.04623 | 0.04623 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02287 | | | 0.48 Nlocal: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14170 ave 14170 max 14170 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: 365610 ave 365610 max 365610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365610 Ave neighs/atom = 209.639 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) = 6.002 | 6.002 | 6.002 Mbytes Step Temp E_pair E_mol TotEng Press Volume 290 0 -5937.0415 0 -5937.0415 -7156.5039 29261.338 1290 0 -5937.395 0 -5937.395 -2290.4601 29081.386 Loop time of 17.734 on 1 procs for 1000 steps with 1744 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 = -5937.04147205 -5937.39499047 -5937.39499047 Force two-norm initial, final = 143.998 0.0079459 Force max component initial, final = 119.538 0.00586246 Final line search alpha, max atom move = 0.485325 0.0028452 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.101 | 17.101 | 17.101 | 0.0 | 96.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15012 | 0.15012 | 0.15012 | 0.0 | 0.85 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4825 | | | 2.72 Nlocal: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14159 ave 14159 max 14159 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: 365544 ave 365544 max 365544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365544 Ave neighs/atom = 209.601 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.139 | 6.139 | 6.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5937.395 0 -5937.395 -2290.4601 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1744 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: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14164 ave 14164 max 14164 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: 371336 ave 371336 max 371336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371336 Ave neighs/atom = 212.922 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) = 6.139 | 6.139 | 6.139 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 -5937.395 -5937.395 60.075178 120.28263 4.0245481 -2290.4601 -2290.4601 -0.32264619 -6870.911 -0.14670648 2.4747068 330.86035 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1744 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: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14164 ave 14164 max 14164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 185668 ave 185668 max 185668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 371336 ave 371336 max 371336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371336 Ave neighs/atom = 212.922 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_084.5474/numatoms.out 1744 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5937.39499047295-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5937.39499047295-1744*${isolated_atom_energy} variable adjusted_pe_metal equal -5937.39499047295-1744*0 print "${adjusted_pe_metal} eV" file output/dump_084.5474/energy.out -5937.39499047295 eV print "${mindist_metal} Angstroms" file output/dump_084.5474/mindistance.out 2.47470678607591 Angstroms write_dump all cfg output/dump_084.5474/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_084.5474/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:22