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 4.050199627876282*${_u_distance} variable lattice_constant_converted equal 4.050199627876282*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 61.290642017143696*${_u_distance} variable xmax_converted equal 61.290642017143696*1 variable ymin_converted equal -61.29469221677157*${_u_distance} variable ymin_converted equal -61.29469221677157*1 variable ymax_converted equal 61.29469221677157*${_u_distance} variable ymax_converted equal 61.29469221677157*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050199627876282*${_u_distance} variable zmax_converted equal 4.050199627876282*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05019962787628 Lattice spacing in x,y,z = 4.0502 4.0502 4.0502 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 61.2906420171437 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.2906420171437 -61.2946922167716 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.2906420171437 -61.2946922167716 61.2946922167716 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.2906420171437 -61.2946922167716 61.2946922167716 0 ${zmax_converted} units box region whole block 0 61.2906420171437 -61.2946922167716 61.2946922167716 0 4.05019962787628 units box create_box 2 whole Created orthogonal box = (0 -61.2947 0) to (61.2906 61.2947 4.0502) 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 61.2946922167716 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.54996 4.54996 4.0502 create_atoms 1 region upper Created 918 atoms create_atoms CPU = 0.000320911 secs group upper type 1 918 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.8097356776897 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.2946922167716 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.54996 4.54996 4.0502 create_atoms 2 region lower Created 918 atoms create_atoms CPU = 0.000219822 secs group lower type 2 918 atoms in group lower displace_atoms lower move -6.8097356776897 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Al__MO_060567868558_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*4.05019962787628 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509981393814 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 15 30 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 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1810 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 15 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.595 | 5.595 | 5.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6459.5675 0 -6459.5675 -1665.0942 113 0 -6470.2083 0 -6470.2083 -2760.1003 Loop time of 1.50917 on 1 procs for 113 steps with 1810 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -6459.56749281 -6470.20828651 -6470.20828651 Force two-norm initial, final = 9.20636 0.0270593 Force max component initial, final = 2.07657 0.0049475 Final line search alpha, max atom move = 1.52588e-05 7.54929e-08 Iterations, force evaluations = 113 248 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4694 | 1.4694 | 1.4694 | 0.0 | 97.36 Neigh | 0.013971 | 0.013971 | 0.013971 | 0.0 | 0.93 Comm | 0.016174 | 0.016174 | 0.016174 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009674 | | | 0.64 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11278 ave 11278 max 11278 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: 253240 ave 253240 max 253240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253240 Ave neighs/atom = 139.912 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) = 5.595 | 5.595 | 5.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -6470.2083 0 -6470.2083 -2760.1003 30431.507 116 0 -6470.262 0 -6470.262 -1015.0194 30360.788 Loop time of 0.203302 on 1 procs for 3 steps with 1810 atoms 103.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -6470.20828651 -6470.26203284 -6470.26203284 Force two-norm initial, final = 51.6089 1.83703 Force max component initial, final = 38.8459 1.55918 Final line search alpha, max atom move = 2.69748e-09 4.20587e-09 Iterations, force evaluations = 3 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19493 | 0.19493 | 0.19493 | 0.0 | 95.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021293 | 0.0021293 | 0.0021293 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006247 | | | 3.07 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11295 ave 11295 max 11295 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: 253520 ave 253520 max 253520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253520 Ave neighs/atom = 140.066 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 15 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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) = 5.733 | 5.733 | 5.733 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6470.262 0 -6470.262 -1015.0194 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1810 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: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11300 ave 11300 max 11300 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: 253612 ave 253612 max 253612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253612 Ave neighs/atom = 140.117 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) = 5.733 | 5.733 | 5.733 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 -6470.262 -6470.262 61.211939 122.58938 4.0459829 -1015.0194 -1015.0194 -51.141477 -3076.1111 82.194292 2.5777365 472.05266 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1810 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 | | 1.192e-06 | | |100.00 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11300 ave 11300 max 11300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126806 ave 126806 max 126806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253612 ave 253612 max 253612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253612 Ave neighs/atom = 140.117 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_015.1893/numatoms.out 1810 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6470.26203284413-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6470.26203284413-1810*${isolated_atom_energy} variable adjusted_pe_metal equal -6470.26203284413-1810*0 print "${adjusted_pe_metal} eV" file output/dump_015.1893/energy.out -6470.26203284413 eV print "${mindist_metal} Angstroms" file output/dump_015.1893/mindistance.out 2.57773647442587 Angstroms write_dump all cfg output/dump_015.1893/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_015.1893/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01