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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 12.727678620088179*${_u_distance} variable xmax_converted equal 12.727678620088179*1 variable ymin_converted equal -50.91473932572933*${_u_distance} variable ymin_converted equal -50.91473932572933*1 variable ymax_converted equal 50.91473932572933*${_u_distance} variable ymax_converted equal 50.91473932572933*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 12.7276786200882 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7276786200882 -50.9147393257293 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7276786200882 -50.9147393257293 50.9147393257293 ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7276786200882 -50.9147393257293 50.9147393257293 0 ${zmax_converted} units box region whole block 0 12.7276786200882 -50.9147393257293 50.9147393257293 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -50.9147 0) to (12.7277 50.9147 4.02485) 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 50.9147393257293 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.09107 5.09107 4.02485 create_atoms 1 region upper Created 162 atoms create_atoms CPU = 0.000209093 secs group upper type 1 162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -50.9147393257293 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.09107 5.09107 4.02485 create_atoms 2 region lower Created 162 atoms create_atoms CPU = 7.29561e-05 secs group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 25 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 318 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -828.47901 0 -828.47901 3124.0824 448 0 -838.75318 0 -838.75318 492.04862 Loop time of 0.942404 on 1 procs for 448 steps with 318 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -828.479009449 -838.75318487 -838.75318487 Force two-norm initial, final = 13.0279 8.35362e-06 Force max component initial, final = 3.42742 2.54425e-06 Final line search alpha, max atom move = 1 2.54425e-06 Iterations, force evaluations = 448 888 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91623 | 0.91623 | 0.91623 | 0.0 | 97.22 Neigh | 0.001256 | 0.001256 | 0.001256 | 0.0 | 0.13 Comm | 0.017388 | 0.017388 | 0.017388 | 0.0 | 1.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007529 | | | 0.80 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3916 ave 3916 max 3916 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: 44436 ave 44436 max 44436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44436 Ave neighs/atom = 139.736 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) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 448 0 -838.75318 0 -838.75318 492.04862 5216.4124 1448 0 -838.75542 0 -838.75542 1474.6549 5209.8896 Loop time of 2.4363 on 1 procs for 1000 steps with 318 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 = -838.75318487 -838.755420926 -838.755420927 Force two-norm initial, final = 5.02632 0.000471998 Force max component initial, final = 3.70016 0.000233703 Final line search alpha, max atom move = 1 0.000233703 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2684 | 2.2684 | 2.2684 | 0.0 | 93.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.041867 | 0.041867 | 0.041867 | 0.0 | 1.72 Output | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.126 | | | 5.17 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023 ave 4023 max 4023 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: 44352 ave 44352 max 44352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44352 Ave neighs/atom = 139.472 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 4.607 | 4.607 | 4.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -838.75542 0 -838.75542 1474.6549 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023 ave 4023 max 4023 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: 44368 ave 44368 max 44368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44368 Ave neighs/atom = 139.522 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) = 4.607 | 4.607 | 4.607 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 -838.75542 -838.75542 12.7186 101.82948 4.0226818 1474.6549 1474.6549 -0.022923451 4423.9158 0.071831209 2.6040273 215.01974 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023 ave 4023 max 4023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22184 ave 22184 max 22184 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44368 ave 44368 max 44368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44368 Ave neighs/atom = 139.522 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -838.755420926973-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -838.755420926973-318*${isolated_atom_energy} variable adjusted_pe_metal equal -838.755420926973-318*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_036.8699/energy.out -828.981925259536 eV print "${mindist_metal} Angstroms" file output/dump_036.8699/mindistance.out 2.60402731713171 Angstroms write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03