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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.40038358692124*${_u_distance} variable xmax_converted equal 67.40038358692124*1 variable ymin_converted equal -67.40443328348591*${_u_distance} variable ymin_converted equal -67.40443328348591*1 variable ymax_converted equal 67.40443328348591*${_u_distance} variable ymax_converted equal 67.40443328348591*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 67.4003835869212 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4003835869212 -67.4044332834859 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4003835869212 -67.4044332834859 67.4044332834859 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.4003835869212 -67.4044332834859 67.4044332834859 0 ${zmax_converted} units box region whole block 0 67.4003835869212 -67.4044332834859 67.4044332834859 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -67.4044 0) to (67.4004 67.4044 4.0497) 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 67.4044332834859 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59642 5.59642 4.0497 create_atoms 1 region upper Created 1110 atoms create_atoms CPU = 0.00028801 secs group upper type 1 1110 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.489492639691956 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -67.4044332834859 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59642 5.59642 4.0497 create_atoms 2 region lower Created 1110 atoms create_atoms CPU = 0.00018692 secs group lower type 2 1110 atoms in group lower displace_atoms lower move -7.489492639691956 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 36 2 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2192 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.65 | 5.65 | 5.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7347.7963 0 -7347.7963 425.57513 397 0 -7371.4883 0 -7371.4883 -5017.3218 Loop time of 4.12788 on 1 procs for 397 steps with 2192 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7347.79628444 -7371.48826191 -7371.48826191 Force two-norm initial, final = 32.7486 1.65708e-05 Force max component initial, final = 6.06795 3.23422e-06 Final line search alpha, max atom move = 1 3.23422e-06 Iterations, force evaluations = 397 780 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0238 | 4.0238 | 4.0238 | 0.0 | 97.48 Neigh | 0.014565 | 0.014565 | 0.014565 | 0.0 | 0.35 Comm | 0.053671 | 0.053671 | 0.053671 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03585 | | | 0.87 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708 ave 12708 max 12708 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: 263316 ave 263316 max 263316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263316 Ave neighs/atom = 120.126 Neighbor list builds = 2 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) = 5.651 | 5.651 | 5.651 Mbytes Step Temp E_pair E_mol TotEng Press Volume 397 0 -7371.4883 0 -7371.4883 -5017.3218 36796.229 1397 0 -7371.7727 0 -7371.7727 -773.66789 36610.818 Loop time of 11.0704 on 1 procs for 1000 steps with 2192 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 = -7371.48826191 -7371.7727279 -7371.77272835 Force two-norm initial, final = 151.672 0.0808387 Force max component initial, final = 114.712 0.0802888 Final line search alpha, max atom move = 0.0159984 0.00128449 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.458 | 10.458 | 10.458 | 0.0 | 94.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13224 | 0.13224 | 0.13224 | 0.0 | 1.19 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4802 | | | 4.34 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12718 ave 12718 max 12718 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: 264296 ave 264296 max 264296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264296 Ave neighs/atom = 120.573 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.789 | 5.789 | 5.789 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7371.7727 0 -7371.7727 -773.66789 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12718 ave 12718 max 12718 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: 272272 ave 272272 max 272272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272272 Ave neighs/atom = 124.212 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) = 5.789 | 5.789 | 5.789 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 -7371.7727 -7371.7727 67.294576 134.80887 4.035626 -773.66789 -773.66789 -0.40125629 -2324.1038 3.5014194 2.5839317 1045.7029 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12718 ave 12718 max 12718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136136 ave 136136 max 136136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272272 ave 272272 max 272272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272272 Ave neighs/atom = 124.212 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_065.4705/numatoms.out 2192 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7371.77272834632-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7371.77272834632-2192*${isolated_atom_energy} variable adjusted_pe_metal equal -7371.77272834632-2192*0 print "${adjusted_pe_metal} eV" file output/dump_065.4705/energy.out -7371.77272834632 eV print "${mindist_metal} Angstroms" file output/dump_065.4705/mindistance.out 2.58393173912921 Angstroms write_dump all cfg output/dump_065.4705/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_065.4705/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15