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 4.210718545317654*${_u_distance} variable lattice_constant_converted equal 4.210718545317654*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 21.47053602882174*${_u_distance} variable xmax_converted equal 21.47053602882174*1 variable ymin_converted equal -42.9452827761888*${_u_distance} variable ymin_converted equal -42.9452827761888*1 variable ymax_converted equal 42.9452827761888*${_u_distance} variable ymax_converted equal 42.9452827761888*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210718545317654*${_u_distance} variable zmax_converted equal 4.210718545317654*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21071854531765 Lattice spacing in x,y,z = 4.21072 4.21072 4.21072 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 21.4705360288217 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4705360288217 -42.9452827761888 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4705360288217 -42.9452827761888 42.9452827761888 ${zmin_converted} ${zmax_converted} units box region whole block 0 21.4705360288217 -42.9452827761888 42.9452827761888 0 ${zmax_converted} units box region whole block 0 21.4705360288217 -42.9452827761888 42.9452827761888 0 4.21071854531765 units box create_box 2 whole Created orthogonal box = (0 -42.9453 0) to (21.4705 42.9453 4.21072) 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 42.9452827761888 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95474 4.95474 4.21072 create_atoms 1 region upper Created 210 atoms create_atoms CPU = 0.000193834 secs group upper type 1 210 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.294558781116753 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.9452827761888 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95474 4.95474 4.21072 create_atoms 2 region lower Created 210 atoms create_atoms CPU = 6.38962e-05 secs group lower type 2 210 atoms in group lower displace_atoms lower move -2.294558781116753 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_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*4.21071854531765 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535927265882 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 20 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 410 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1522.1939 0 -1522.1939 544.20743 222 0 -1525.7039 0 -1525.7039 -1916.2361 Loop time of 0.650211 on 1 procs for 222 steps with 410 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 = -1522.19387206 -1525.70392949 -1525.70392949 Force two-norm initial, final = 8.77257 9.65553e-06 Force max component initial, final = 2.77707 1.38569e-06 Final line search alpha, max atom move = 1 1.38569e-06 Iterations, force evaluations = 222 437 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63641 | 0.63641 | 0.63641 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0093627 | 0.0093627 | 0.0093627 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004441 | | | 0.68 Nlocal: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4130 ave 4130 max 4130 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: 70772 ave 70772 max 70772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70772 Ave neighs/atom = 172.615 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -1525.7039 0 -1525.7039 -1916.2361 7765.0555 1222 0 -1525.724 0 -1525.724 -198.61586 7730.8006 Loop time of 3.15839 on 1 procs for 1000 steps with 410 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 = -1525.70392949 -1525.72404081 -1525.72404081 Force two-norm initial, final = 12.9077 0.000826722 Force max component initial, final = 9.13565 0.000566035 Final line search alpha, max atom move = 1 0.000566035 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9781 | 2.9781 | 2.9781 | 0.0 | 94.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045313 | 0.045313 | 0.045313 | 0.0 | 1.43 Output | 4.1008e-05 | 4.1008e-05 | 4.1008e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1349 | | | 4.27 Nlocal: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4591 ave 4591 max 4591 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: 70320 ave 70320 max 70320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70320 Ave neighs/atom = 171.512 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 -0.09604918 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1525.724 0 -1525.724 -198.61586 Loop time of 9.53674e-07 on 1 procs for 0 steps with 410 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: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4599 ave 4599 max 4599 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: 70432 ave 70432 max 70432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70432 Ave neighs/atom = 171.785 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) = 4.619 | 4.619 | 4.619 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 -1525.724 -1525.724 21.423038 85.890566 4.201438 -198.61586 -198.61586 -0.059584289 -595.67095 -0.11704989 2.7313141 453.14789 Loop time of 9.53674e-07 on 1 procs for 0 steps with 410 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: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4599 ave 4599 max 4599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35216 ave 35216 max 35216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70432 ave 70432 max 70432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70432 Ave neighs/atom = 171.785 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_022.6199/numatoms.out 410 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1525.72404081095-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1525.72404081095-410*${isolated_atom_energy} variable adjusted_pe_metal equal -1525.72404081095-410*-0.09604918 print "${adjusted_pe_metal} eV" file output/dump_022.6199/energy.out -1486.34387701095 eV print "${mindist_metal} Angstroms" file output/dump_022.6199/mindistance.out 2.73131407945097 Angstroms write_dump all cfg output/dump_022.6199/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_022.6199/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03