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 4.051526293158533*${_u_distance} variable lattice_constant_converted equal 4.051526293158533*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 45.2974410206511*${_u_distance} variable xmax_converted equal 45.2974410206511*1 variable ymin_converted equal -45.30149254694426*${_u_distance} variable ymin_converted equal -45.30149254694426*1 variable ymax_converted equal 45.30149254694426*${_u_distance} variable ymax_converted equal 45.30149254694426*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.051526293158533*${_u_distance} variable zmax_converted equal 4.051526293158533*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05152629315853 Lattice spacing in x,y,z = 4.05153 4.05153 4.05153 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 45.2974410206511 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2974410206511 -45.3014925469443 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2974410206511 -45.3014925469443 45.3014925469443 ${zmin_converted} ${zmax_converted} units box region whole block 0 45.2974410206511 -45.3014925469443 45.3014925469443 0 ${zmax_converted} units box region whole block 0 45.2974410206511 -45.3014925469443 45.3014925469443 0 4.05152629315853 units box create_box 2 whole Created orthogonal box = (0 -45.3015 0) to (45.2974 45.3015 4.05153) 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 45.3014925469443 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.71093 4.71093 4.05153 create_atoms 1 region upper Created 502 atoms create_atoms CPU = 0.00027585 secs group upper type 1 502 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.031152949374526 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.3014925469443 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.71093 4.71093 4.05153 create_atoms 2 region lower Created 502 atoms create_atoms CPU = 0.000128031 secs group lower type 2 502 atoms in group lower displace_atoms lower move -5.031152949374526 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_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*4.05152629315853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02576314657927 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 12 23 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 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 984 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3268.7104 0 -3268.7104 6033.6354 301 0 -3289.4527 0 -3289.4527 -3555.6806 Loop time of 1.72199 on 1 procs for 301 steps with 984 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3268.71043013 -3289.45271526 -3289.45271526 Force two-norm initial, final = 45.3656 1.38231e-05 Force max component initial, final = 11.1504 2.68613e-06 Final line search alpha, max atom move = 1 2.68613e-06 Iterations, force evaluations = 301 596 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.683 | 1.683 | 1.683 | 0.0 | 97.73 Neigh | 0.00336 | 0.00336 | 0.00336 | 0.0 | 0.20 Comm | 0.022417 | 0.022417 | 0.022417 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01323 | | | 0.77 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6816 ave 6816 max 6816 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: 129716 ave 129716 max 129716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129716 Ave neighs/atom = 131.825 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) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 301 0 -3289.4527 0 -3289.4527 -3555.6806 16627.802 1301 0 -3289.5054 0 -3289.5054 -665.6434 16577.565 Loop time of 5.8733 on 1 procs for 1000 steps with 984 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 = -3289.45271526 -3289.50536473 -3289.50536475 Force two-norm initial, final = 47.9034 0.015549 Force max component initial, final = 36.6082 0.0107256 Final line search alpha, max atom move = 0.155962 0.00167279 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5622 | 5.5622 | 5.5622 | 0.0 | 94.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069227 | 0.069227 | 0.069227 | 0.0 | 1.18 Output | 1.3828e-05 | 1.3828e-05 | 1.3828e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2418 | | | 4.12 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6811 ave 6811 max 6811 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: 129736 ave 129736 max 129736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129736 Ave neighs/atom = 131.846 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 -9.23201098901316e-12 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3289.5054 0 -3289.5054 -665.6434 Loop time of 9.53674e-07 on 1 procs for 0 steps with 984 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: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6816 ave 6816 max 6816 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: 129808 ave 129808 max 129808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129808 Ave neighs/atom = 131.919 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) = 5.127 | 5.127 | 5.127 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 -3289.5054 -3289.5054 45.252192 90.602985 4.0433247 -665.6434 -665.6434 -1.0355663 -1995.3443 -0.55029683 2.6034743 748.31729 Loop time of 2.14577e-06 on 1 procs for 0 steps with 984 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 | | 2.146e-06 | | |100.00 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6816 ave 6816 max 6816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64904 ave 64904 max 64904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129808 ave 129808 max 129808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129808 Ave neighs/atom = 131.919 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_020.6097/numatoms.out 984 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3289.50536474514-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3289.50536474514-984*${isolated_atom_energy} variable adjusted_pe_metal equal -3289.50536474514-984*-9.23201098901316e-12 print "${adjusted_pe_metal} eV" file output/dump_020.6097/energy.out -3289.50536473606 eV print "${mindist_metal} Angstroms" file output/dump_020.6097/mindistance.out 2.60347429415554 Angstroms write_dump all cfg output/dump_020.6097/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_020.6097/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:07