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 55.106715391762016*${_u_distance} variable xmax_converted equal 55.106715391762016*1 variable ymin_converted equal -55.11076691805518*${_u_distance} variable ymin_converted equal -55.11076691805518*1 variable ymax_converted equal 55.11076691805518*${_u_distance} variable ymax_converted equal 55.11076691805518*1 variable zmin_converted equal 0.0*${_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 55.106715391762 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.106715391762 -55.1107669180552 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.106715391762 -55.1107669180552 55.1107669180552 ${zmin_converted} ${zmax_converted} units box region whole block 0 55.106715391762 -55.1107669180552 55.1107669180552 0 ${zmax_converted} units box region whole block 0 55.106715391762 -55.1107669180552 55.1107669180552 0 4.05152629315853 units box create_box 2 whole Created orthogonal box = (0 -55.1108 0) to (55.1067 55.1108 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 55.1107669180552 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -8 0 orient y 8 11 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 11 -8 0 orient y 8 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.65961 5.65961 4.05153 create_atoms 1 region upper Created 742 atoms create_atoms CPU = 0.000345945 secs group upper type 1 742 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.1206617289309495 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -55.1107669180552 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 8 0 orient y -8 11 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 11 8 0 orient y -8 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.65961 5.65961 4.05153 create_atoms 2 region lower Created 742 atoms create_atoms CPU = 0.000205994 secs group lower type 2 742 atoms in group lower displace_atoms lower move -6.1206617289309495 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 14 28 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 24 atoms, new total = 1460 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 = 14 28 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4827.3088 0 -4827.3088 11325.949 245 0 -4887.9763 0 -4887.9763 -4868.1037 Loop time of 2.15563 on 1 procs for 245 steps with 1460 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4827.30883612 -4887.97632052 -4887.97632052 Force two-norm initial, final = 98.4879 4.27225e-05 Force max component initial, final = 26.7561 4.93685e-06 Final line search alpha, max atom move = 1 4.93685e-06 Iterations, force evaluations = 245 469 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0991 | 2.0991 | 2.0991 | 0.0 | 97.38 Neigh | 0.015427 | 0.015427 | 0.015427 | 0.0 | 0.72 Comm | 0.025429 | 0.025429 | 0.025429 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01566 | | | 0.73 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9241 ave 9241 max 9241 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: 193520 ave 193520 max 193520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193520 Ave neighs/atom = 132.548 Neighbor list builds = 3 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 245 0 -4887.9763 0 -4887.9763 -4868.1037 24608.755 1245 0 -4888.0599 0 -4888.0599 -2125.8366 24537.847 Loop time of 8.77635 on 1 procs for 1000 steps with 1460 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4887.97632052 -4888.0599308 -4888.05993081 Force two-norm initial, final = 68.5906 0.0100327 Force max component initial, final = 58.6875 0.00698095 Final line search alpha, max atom move = 0.0563463 0.000393351 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3536 | 8.3536 | 8.3536 | 0.0 | 95.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.093752 | 0.093752 | 0.093752 | 0.0 | 1.07 Output | 1.9789e-05 | 1.9789e-05 | 1.9789e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.329 | | | 3.75 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9191 ave 9191 max 9191 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: 193592 ave 193592 max 193592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193592 Ave neighs/atom = 132.597 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 = 14 28 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4888.0599 0 -4888.0599 -2125.8366 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9210 ave 9210 max 9210 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: 193616 ave 193616 max 193616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193616 Ave neighs/atom = 132.614 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) = 5.235 | 5.235 | 5.235 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 -4888.0599 -4888.0599 55.101122 110.22153 4.0402622 -2125.8366 -2125.8366 -0.42330668 -6377.5411 0.45454757 2.6308763 610.75987 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9210 ave 9210 max 9210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96808 ave 96808 max 96808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193616 ave 193616 max 193616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193616 Ave neighs/atom = 132.614 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.0547/numatoms.out 1460 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4888.05993081035-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4888.05993081035-1460*${isolated_atom_energy} variable adjusted_pe_metal equal -4888.05993081035-1460*-9.23201098901316e-12 print "${adjusted_pe_metal} eV" file output/dump_072.0547/energy.out -4888.05993079687 eV print "${mindist_metal} Angstroms" file output/dump_072.0547/mindistance.out 2.63087628509835 Angstroms write_dump all cfg output/dump_072.0547/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_072.0547/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11