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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 53.150089437459016*${_u_distance} variable xmax_converted equal 53.150089437459016*1 variable ymin_converted equal -53.15413036393037*${_u_distance} variable ymin_converted equal -53.15413036393037*1 variable ymax_converted equal 53.15413036393037*${_u_distance} variable ymax_converted equal 53.15413036393037*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 53.150089437459 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.150089437459 -53.1541303639304 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.150089437459 -53.1541303639304 53.1541303639304 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.150089437459 -53.1541303639304 53.1541303639304 0 ${zmax_converted} units box region whole block 0 53.150089437459 -53.1541303639304 53.1541303639304 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -53.1541 0) to (53.1501 53.1541 4.04093) 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 53.1541303639304 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.60839 4.60839 4.04093 create_atoms 1 region upper Created 694 atoms create_atoms CPU = 0.000277996 secs group upper type 1 694 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.918825897084657 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.1541303639304 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.60839 4.60839 4.04093 create_atoms 2 region lower Created 694 atoms create_atoms CPU = 0.000147104 secs group lower type 2 694 atoms in group lower displace_atoms lower move -5.918825897084657 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1364 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.92 | 5.92 | 5.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5297.8386 0 -5297.8386 -644.34415 489 0 -5310.8019 0 -5310.8019 -5345.2912 Loop time of 9.28033 on 1 procs for 489 steps with 1364 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 = -5297.83858651 -5310.80192752 -5310.80192752 Force two-norm initial, final = 17.2753 1.02934e-05 Force max component initial, final = 5.38966 2.32629e-06 Final line search alpha, max atom move = 1 2.32629e-06 Iterations, force evaluations = 489 973 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.171 | 9.171 | 9.171 | 0.0 | 98.82 Neigh | 0.00843 | 0.00843 | 0.00843 | 0.0 | 0.09 Comm | 0.069039 | 0.069039 | 0.069039 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03191 | | | 0.34 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11972 ave 11972 max 11972 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: 333484 ave 333484 max 333484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 333484 Ave neighs/atom = 244.49 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) = 5.92 | 5.92 | 5.92 Mbytes Step Temp E_pair E_mol TotEng Press Volume 489 0 -5310.8019 0 -5310.8019 -5345.2912 22832.421 1489 0 -5310.9687 0 -5310.9687 -1245.8636 22717.111 Loop time of 18.5627 on 1 procs for 1000 steps with 1364 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 = -5310.80192752 -5310.96871701 -5310.96871708 Force two-norm initial, final = 92.0827 0.0271519 Force max component initial, final = 68.1176 0.02106 Final line search alpha, max atom move = 0.021688 0.000456749 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.038 | 18.038 | 18.038 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12594 | 0.12594 | 0.12594 | 0.0 | 0.68 Output | 3.9816e-05 | 3.9816e-05 | 3.9816e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3986 | | | 2.15 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11916 ave 11916 max 11916 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: 332228 ave 332228 max 332228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332228 Ave neighs/atom = 243.569 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.057 | 6.057 | 6.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5310.9687 0 -5310.9687 -1245.8636 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11950 ave 11950 max 11950 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: 333044 ave 333044 max 333044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 333044 Ave neighs/atom = 244.167 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) = 6.057 | 6.057 | 6.057 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 -5310.9687 -5310.9687 53.037232 106.30826 4.029074 -1245.8636 -1245.8636 1.4821522 -3738.081 -0.9919547 2.5162981 791.41072 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11950 ave 11950 max 11950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166522 ave 166522 max 166522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 333044 ave 333044 max 333044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 333044 Ave neighs/atom = 244.167 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_017.4923/numatoms.out 1364 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5310.96871708487-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5310.96871708487-1364*${isolated_atom_energy} variable adjusted_pe_metal equal -5310.96871708487-1364*0 print "${adjusted_pe_metal} eV" file output/dump_017.4923/energy.out -5310.96871708487 eV print "${mindist_metal} Angstroms" file output/dump_017.4923/mindistance.out 2.51629811245117 Angstroms write_dump all cfg output/dump_017.4923/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_017.4923/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:27