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 52.805600799235975*${_u_distance} variable xmax_converted equal 52.805600799235975*1 variable ymin_converted equal -52.80965080393878*${_u_distance} variable ymin_converted equal -52.80965080393878*1 variable ymax_converted equal 52.80965080393878*${_u_distance} variable ymax_converted equal 52.80965080393878*1 variable zmin_converted equal 0.0*${_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 52.805600799236 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.805600799236 -52.8096508039388 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.805600799236 -52.8096508039388 52.8096508039388 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.805600799236 -52.8096508039388 52.8096508039388 0 ${zmax_converted} units box region whole block 0 52.805600799236 -52.8096508039388 52.8096508039388 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -52.8097 0) to (52.8056 52.8097 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 52.8096508039388 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3487 4.3487 4.05 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000204086 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_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 -52.8096508039388 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3487 4.3487 4.05 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 8.91685e-05 secs group lower type 2 682 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_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 = 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 8.28721 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4475.6755 0 -4475.6755 -1798.8761 210 0 -4490.7765 0 -4490.7765 -8955.3779 Loop time of 1.43174 on 1 procs for 210 steps with 1340 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4475.67548158 -4490.77645084 -4490.77645084 Force two-norm initial, final = 11.6826 2.25439e-07 Force max component initial, final = 2.77281 3.43432e-08 Final line search alpha, max atom move = 1 3.43432e-08 Iterations, force evaluations = 210 411 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4024 | 1.4024 | 1.4024 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018327 | 0.018327 | 0.018327 | 0.0 | 1.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01103 | | | 0.77 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8810 ave 8810 max 8810 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: 185164 ave 185164 max 185164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185164 Ave neighs/atom = 138.182 Neighbor list builds = 0 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press Volume 210 0 -4490.7765 0 -4490.7765 -8955.3779 22588.053 1210 0 -4491.1534 0 -4491.1534 -2832.67 22412.049 Loop time of 8.10316 on 1 procs for 1000 steps with 1340 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4490.77645084 -4491.15344103 -4491.15344103 Force two-norm initial, final = 135.993 0.00508275 Force max component initial, final = 97.7939 0.00474142 Final line search alpha, max atom move = 0.9966 0.0047253 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7032 | 7.7032 | 7.7032 | 0.0 | 95.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.089857 | 0.089857 | 0.089857 | 0.0 | 1.11 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.31 | | | 3.83 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8847 ave 8847 max 8847 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: 187064 ave 187064 max 187064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187064 Ave neighs/atom = 139.6 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 = 13 26 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) = 5.227 | 5.227 | 5.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4491.1534 0 -4491.1534 -2832.67 Loop time of 2.14577e-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 | | 2.146e-06 | | |100.00 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8869 ave 8869 max 8869 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: 187184 ave 187184 max 187184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187184 Ave neighs/atom = 139.69 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) = 5.227 | 5.227 | 5.227 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 -4491.1534 -4491.1534 52.588205 105.6193 4.0350593 -2832.67 -2832.67 -0.033708301 -8498.3139 0.33770023 2.6262306 318.63801 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: 8869 ave 8869 max 8869 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93592 ave 93592 max 93592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187184 ave 187184 max 187184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187184 Ave neighs/atom = 139.69 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -4491.15344102765-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4491.15344102765-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -4491.15344102765-1340*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4491.15344116731 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.62623063186864 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: 0:00:09