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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.68723514257755*${_u_distance} variable xmax_converted equal 52.68723514257755*1 variable ymin_converted equal -52.691276069048904*${_u_distance} variable ymin_converted equal -52.691276069048904*1 variable ymax_converted equal 52.691276069048904*${_u_distance} variable ymax_converted equal 52.691276069048904*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 52.6872351425775 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6872351425775 -52.6912760690489 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6872351425775 -52.6912760690489 52.6912760690489 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6872351425775 -52.6912760690489 52.6912760690489 0 ${zmax_converted} units box region whole block 0 52.6872351425775 -52.6912760690489 52.6912760690489 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -52.6913 0) to (52.6872 52.6913 4.04093) 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 52.6912760690489 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -7 0 orient y 7 11 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 11 -7 0 orient y 7 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57865 5.57865 4.04093 create_atoms 1 region upper Created 681 atoms create_atoms CPU = 0.000303984 secs group upper type 1 681 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.8672821646823845 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.6912760690489 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 7 0 orient y -7 11 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 11 7 0 orient y -7 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57865 5.57865 4.04093 create_atoms 2 region lower Created 681 atoms create_atoms CPU = 0.000169992 secs group lower type 2 681 atoms in group lower displace_atoms lower move -5.8672821646823845 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1340 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.896 | 5.896 | 5.896 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5199.6845 0 -5199.6845 -178.55828 262 0 -5217.9386 0 -5217.9386 -5941.546 Loop time of 4.89917 on 1 procs for 262 steps with 1340 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 = -5199.6845096 -5217.93856208 -5217.93856208 Force two-norm initial, final = 20.5281 6.27142e-07 Force max component initial, final = 4.40996 1.27972e-07 Final line search alpha, max atom move = 1 1.27972e-07 Iterations, force evaluations = 262 516 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8372 | 4.8372 | 4.8372 | 0.0 | 98.73 Neigh | 0.0078249 | 0.0078249 | 0.0078249 | 0.0 | 0.16 Comm | 0.03673 | 0.03673 | 0.03673 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01743 | | | 0.36 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11818 ave 11818 max 11818 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: 327638 ave 327638 max 327638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327638 Ave neighs/atom = 244.506 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) = 5.896 | 5.896 | 5.896 Mbytes Step Temp E_pair E_mol TotEng Press Volume 262 0 -5217.9386 0 -5217.9386 -5941.546 22436.498 1262 0 -5218.1511 0 -5218.1511 -1333.7786 22309.807 Loop time of 18.4462 on 1 procs for 1000 steps with 1340 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 = -5217.93856208 -5218.15108392 -5218.15108397 Force two-norm initial, final = 103.724 0.0159446 Force max component initial, final = 78.4751 0.0121579 Final line search alpha, max atom move = 0.0546536 0.000664475 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.919 | 17.919 | 17.919 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12683 | 0.12683 | 0.12683 | 0.0 | 0.69 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4006 | | | 2.17 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11824 ave 11824 max 11824 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: 328648 ave 328648 max 328648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328648 Ave neighs/atom = 245.26 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.034 | 6.034 | 6.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5218.1511 0 -5218.1511 -1333.7786 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11824 ave 11824 max 11824 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: 329084 ave 329084 max 329084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329084 Ave neighs/atom = 245.585 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) = 6.034 | 6.034 | 6.034 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 -5218.1511 -5218.1511 52.585968 105.38255 4.0258466 -1333.7786 -1333.7786 0.87144144 -4002.2335 0.026187498 2.4890711 865.47593 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11824 ave 11824 max 11824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164542 ave 164542 max 164542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 329084 ave 329084 max 329084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329084 Ave neighs/atom = 245.585 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_064.9424/numatoms.out 1340 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5218.15108396804-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5218.15108396804-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -5218.15108396804-1340*0 print "${adjusted_pe_metal} eV" file output/dump_064.9424/energy.out -5218.15108396804 eV print "${mindist_metal} Angstroms" file output/dump_064.9424/mindistance.out 2.48907111132606 Angstroms write_dump all cfg output/dump_064.9424/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_064.9424/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:23