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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 30.843872601504287*${_u_distance} variable xmax_converted equal 30.843872601504287*1 variable ymin_converted equal -61.69179520189546*${_u_distance} variable ymin_converted equal -61.69179520189546*1 variable ymax_converted equal 61.69179520189546*${_u_distance} variable ymax_converted equal 61.69179520189546*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 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 30.8438726015043 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 0 ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -61.6918 0) to (30.8439 61.6918 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 61.6917952018955 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31791 5.31791 4.05 create_atoms 1 region upper Created 466 atoms create_atoms CPU = 0.000205994 secs group upper type 1 466 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.4270978976387587 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.6917952018955 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31791 5.31791 4.05 create_atoms 2 region lower Created 466 atoms create_atoms CPU = 9.20296e-05 secs group lower type 2 466 atoms in group lower displace_atoms lower move -3.4270978976387587 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_811588957187_000-files/b'library-Al.meam' Al ./SM_811588957187_000-files/b'Al.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 16 atoms, new total = 916 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3051.6712 0 -3051.6712 2337.0078 332 0 -3066.7194 0 -3066.7194 -3794.0656 Loop time of 6.04928 on 1 procs for 332 steps with 916 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3051.67118178 -3066.71944004 -3066.71944004 Force two-norm initial, final = 23.5598 1.06343e-05 Force max component initial, final = 6.90134 1.90894e-06 Final line search alpha, max atom move = 1 1.90894e-06 Iterations, force evaluations = 332 658 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.01 | 6.01 | 6.01 | 0.0 | 99.35 Neigh | 0.0019701 | 0.0019701 | 0.0019701 | 0.0 | 0.03 Comm | 0.022413 | 0.022413 | 0.022413 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01493 | | | 0.25 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5707 ave 5707 max 5707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35888 ave 35888 max 35888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71776 ave 71776 max 71776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71776 Ave neighs/atom = 78.3581 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) = 11.89 | 11.89 | 11.89 Mbytes Step Temp E_pair E_mol TotEng Press Volume 332 0 -3066.7194 0 -3066.7194 -3794.0656 15412.788 1332 0 -3066.795 0 -3066.795 -655.16591 15348.08 Loop time of 19.0656 on 1 procs for 1000 steps with 916 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3066.71944004 -3066.79501204 -3066.79501215 Force two-norm initial, final = 48.612 0.0342825 Force max component initial, final = 37.8531 0.0310221 Final line search alpha, max atom move = 0.155173 0.00481379 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.788 | 18.788 | 18.788 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060771 | 0.060771 | 0.060771 | 0.0 | 0.32 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2169 | | | 1.14 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5592 ave 5592 max 5592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36106 ave 36106 max 36106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72212 ave 72212 max 72212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72212 Ave neighs/atom = 78.8341 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.79 | 10.79 | 10.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3066.795 0 -3066.795 -655.16591 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36814 ave 36814 max 36814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73628 ave 73628 max 73628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73628 Ave neighs/atom = 80.3799 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) = 10.79 | 10.79 | 10.79 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 -3066.795 -3066.795 30.807862 123.38359 4.0377096 -655.16591 -655.16591 -3.234593 -1961.9007 -0.36240463 2.5174148 530.74085 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36814 ave 36814 max 36814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73628 ave 73628 max 73628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73628 Ave neighs/atom = 80.3799 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_046.3972/numatoms.out 916 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79501214556-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79501214556-916*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79501214556-916*0 print "${adjusted_pe_metal} eV" file output/dump_046.3972/energy.out -3066.79501214556 eV print "${mindist_metal} Angstroms" file output/dump_046.3972/mindistance.out 2.51741483973584 Angstroms write_dump all cfg output/dump_046.3972/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_046.3972/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:25