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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 48.87905991115296*${_u_distance} variable xmax_converted equal 48.87905991115296*1 variable ymin_converted equal -48.88310517093414*${_u_distance} variable ymin_converted equal -48.88310517093414*1 variable ymax_converted equal 48.88310517093414*${_u_distance} variable ymax_converted equal 48.88310517093414*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 48.879059911153 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.879059911153 -48.8831051709341 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.879059911153 -48.8831051709341 48.8831051709341 ${zmin_converted} ${zmax_converted} units box region whole block 0 48.879059911153 -48.8831051709341 48.8831051709341 0 ${zmax_converted} units box region whole block 0 48.879059911153 -48.8831051709341 48.8831051709341 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -48.8831 0) to (48.8791 48.8831 4.04526) 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 48.8831051709341 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.35661 5.35661 4.04526 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000214815 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.437370688117558 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -48.8831051709341 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.35661 5.35661 4.04526 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.000100136 secs group lower type 2 586 atoms in group lower displace_atoms lower move -5.437370688117558 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 24 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1150 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3895.3105 0 -3895.3105 -1554.049 341 0 -3907.7605 0 -3907.7605 -6016.1045 Loop time of 2.90068 on 1 procs for 341 steps with 1150 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 = -3895.31045984 -3907.76050131 -3907.76050131 Force two-norm initial, final = 18.5465 1.7686e-05 Force max component initial, final = 4.36665 3.74069e-06 Final line search alpha, max atom move = 1 3.74069e-06 Iterations, force evaluations = 341 667 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8467 | 2.8467 | 2.8467 | 0.0 | 98.14 Neigh | 0.0076838 | 0.0076838 | 0.0076838 | 0.0 | 0.26 Comm | 0.029219 | 0.029219 | 0.029219 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01712 | | | 0.59 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7925 ave 7925 max 7925 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: 162080 ave 162080 max 162080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162080 Ave neighs/atom = 140.939 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 341 0 -3907.7605 0 -3907.7605 -6016.1045 19331.166 1341 0 -3908.1276 0 -3908.1276 -750.37134 19202.868 Loop time of 8.94926 on 1 procs for 1000 steps with 1150 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3907.76050131 -3908.12760912 -3908.12761862 Force two-norm initial, final = 100.661 0.269969 Force max component initial, final = 79.9126 0.219486 Final line search alpha, max atom move = 0.00944211 0.00207241 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5815 | 8.5815 | 8.5815 | 0.0 | 95.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.082027 | 0.082027 | 0.082027 | 0.0 | 0.92 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2857 | | | 3.19 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7920 ave 7920 max 7920 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: 161764 ave 161764 max 161764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161764 Ave neighs/atom = 140.664 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.186 | 5.186 | 5.186 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3908.1276 0 -3908.1276 -750.37134 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1150 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: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930 ave 7930 max 7930 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: 162260 ave 162260 max 162260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162260 Ave neighs/atom = 141.096 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) = 5.186 | 5.186 | 5.186 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 -3908.1276 -3908.1276 48.789075 97.76621 4.0258234 -750.37134 -750.37134 -0.9799432 -2268.3587 18.22464 2.4984917 911.07797 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1150 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: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930 ave 7930 max 7930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81130 ave 81130 max 81130 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162260 ave 162260 max 162260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162260 Ave neighs/atom = 141.096 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_048.8879/numatoms.out 1150 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3908.12761861973-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3908.12761861973-1150*${isolated_atom_energy} variable adjusted_pe_metal equal -3908.12761861973-1150*0 print "${adjusted_pe_metal} eV" file output/dump_048.8879/energy.out -3908.12761861973 eV print "${mindist_metal} Angstroms" file output/dump_048.8879/mindistance.out 2.49849165024921 Angstroms write_dump all cfg output/dump_048.8879/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_048.8879/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11