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 4.050004702806472*${_u_distance} variable lattice_constant_converted equal 4.050004702806472*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 48.76851467339772*${_u_distance} variable xmax_converted equal 48.76851467339772*1 variable ymin_converted equal -48.77256467810052*${_u_distance} variable ymin_converted equal -48.77256467810052*1 variable ymax_converted equal 48.77256467810052*${_u_distance} variable ymax_converted equal 48.77256467810052*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050004702806472*${_u_distance} variable zmax_converted equal 4.050004702806472*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000470280647 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 48.7685146733977 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7685146733977 -48.7725646781005 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7685146733977 -48.7725646781005 48.7725646781005 ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7685146733977 -48.7725646781005 48.7725646781005 0 ${zmax_converted} units box region whole block 0 48.7685146733977 -48.7725646781005 48.7725646781005 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -48.7726 0) to (48.7685 48.7726 4.05) 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 48.7725646781005 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -8 0 orient y 8 9 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 9 -8 0 orient y 8 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71769 5.71769 4.05 create_atoms 1 region upper Created 582 atoms create_atoms CPU = 0.000298023 secs group upper type 1 582 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.418717560456534 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -48.7725646781005 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 8 0 orient y -8 9 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 9 8 0 orient y -8 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71769 5.71769 4.05 create_atoms 2 region lower Created 582 atoms create_atoms CPU = 0.000194073 secs group lower type 2 582 atoms in group lower displace_atoms lower move -5.418717560456534 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_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*4.05000470280647 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500235140324 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 24 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1144 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3814.545 0 -3814.545 -960.31579 214 0 -3834.4963 0 -3834.4963 -8224.742 Loop time of 1.5537 on 1 procs for 214 steps with 1144 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3814.54498776 -3834.49625743 -3834.49625743 Force two-norm initial, final = 15.1225 2.41947e-06 Force max component initial, final = 2.84787 7.17248e-07 Final line search alpha, max atom move = 1 7.17248e-07 Iterations, force evaluations = 214 419 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5191 | 1.5191 | 1.5191 | 0.0 | 97.77 Neigh | 0.0045729 | 0.0045729 | 0.0045729 | 0.0 | 0.29 Comm | 0.018864 | 0.018864 | 0.018864 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01116 | | | 0.72 Nlocal: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7806 ave 7806 max 7806 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: 159380 ave 159380 max 159380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159380 Ave neighs/atom = 139.318 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) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press Volume 214 0 -3834.4963 0 -3834.4963 -8224.742 19266.403 1214 0 -3834.8221 0 -3834.8221 -2133.1779 19116.212 Loop time of 6.6401 on 1 procs for 1000 steps with 1144 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 = -3834.49625743 -3834.82205703 -3834.82205709 Force two-norm initial, final = 117.524 0.0215246 Force max component initial, final = 83.9774 0.0171559 Final line search alpha, max atom move = 0.370681 0.00635937 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3026 | 6.3026 | 6.3026 | 0.0 | 94.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.076999 | 0.076999 | 0.076999 | 0.0 | 1.16 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2605 | | | 3.92 Nlocal: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7816 ave 7816 max 7816 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: 159336 ave 159336 max 159336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159336 Ave neighs/atom = 139.28 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 1.04222210722815e-10 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.182 | 5.182 | 5.182 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3834.8221 0 -3834.8221 -2133.1779 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1144 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: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7831 ave 7831 max 7831 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: 159516 ave 159516 max 159516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159516 Ave neighs/atom = 139.437 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) = 5.182 | 5.182 | 5.182 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 -3834.8221 -3834.8221 48.59323 97.545129 4.0329281 -2133.1779 -2133.1779 1.4327102 -6401.4578 0.49140548 2.5232867 431.11437 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1144 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: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7831 ave 7831 max 7831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79758 ave 79758 max 79758 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159516 ave 159516 max 159516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159516 Ave neighs/atom = 139.437 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_083.2671/numatoms.out 1144 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3834.82205708739-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3834.82205708739-1144*${isolated_atom_energy} variable adjusted_pe_metal equal -3834.82205708739-1144*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_083.2671/energy.out -3834.82205720662 eV print "${mindist_metal} Angstroms" file output/dump_083.2671/mindistance.out 2.52328670073867 Angstroms write_dump all cfg output/dump_083.2671/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_083.2671/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08