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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 46.17364502150128*${_u_distance} variable xmax_converted equal 46.17364502150128*1 variable ymin_converted equal -46.17769471806595*${_u_distance} variable ymin_converted equal -46.17769471806595*1 variable ymax_converted equal 46.17769471806595*${_u_distance} variable ymax_converted equal 46.17769471806595*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 46.1736450215013 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 46.1736450215013 -46.177694718066 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 46.1736450215013 -46.177694718066 46.177694718066 ${zmin_converted} ${zmax_converted} units box region whole block 0 46.1736450215013 -46.177694718066 46.177694718066 0 ${zmax_converted} units box region whole block 0 46.1736450215013 -46.177694718066 46.177694718066 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -46.1777 0) to (46.1736 46.1777 4.0497) 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 46.177694718066 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68291 5.68291 4.0497 create_atoms 1 region upper Created 521 atoms create_atoms CPU = 0.000298977 secs group upper type 1 521 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.13078941294612 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -46.177694718066 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 7 0 orient y -7 9 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 9 7 0 orient y -7 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68291 5.68291 4.0497 create_atoms 2 region lower Created 521 atoms create_atoms CPU = 0.000164032 secs group lower type 2 521 atoms in group lower displace_atoms lower move -5.13078941294612 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 13 25 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1020 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 13 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.993 | 4.993 | 4.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3412.313 0 -3412.313 -1911.0714 287 0 -3427.9871 0 -3427.9871 -10441.991 Loop time of 1.45299 on 1 procs for 287 steps with 1020 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3412.31297204 -3427.98709159 -3427.98709159 Force two-norm initial, final = 22.2415 9.61834e-06 Force max component initial, final = 6.08989 1.8427e-06 Final line search alpha, max atom move = 1 1.8427e-06 Iterations, force evaluations = 287 556 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4047 | 1.4047 | 1.4047 | 0.0 | 96.68 Neigh | 0.013513 | 0.013513 | 0.013513 | 0.0 | 0.93 Comm | 0.021489 | 0.021489 | 0.021489 | 0.0 | 1.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01324 | | | 0.91 Nlocal: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6870 ave 6870 max 6870 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: 112494 ave 112494 max 112494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112494 Ave neighs/atom = 110.288 Neighbor list builds = 4 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 287 0 -3427.9871 0 -3427.9871 -10441.991 17269.465 1287 0 -3428.5434 0 -3428.5434 -2154.6422 17084.931 Loop time of 5.00753 on 1 procs for 1000 steps with 1020 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 = -3427.98709159 -3428.54342352 -3428.5434241 Force two-norm initial, final = 140.232 0.0542815 Force max component initial, final = 106.65 0.0492936 Final line search alpha, max atom move = 0.012952 0.000638449 Iterations, force evaluations = 1000 1993 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6929 | 4.6929 | 4.6929 | 0.0 | 93.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069452 | 0.069452 | 0.069452 | 0.0 | 1.39 Output | 1.3113e-05 | 1.3113e-05 | 1.3113e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2452 | | | 4.90 Nlocal: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6875 ave 6875 max 6875 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: 111320 ave 111320 max 111320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111320 Ave neighs/atom = 109.137 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 13 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3428.5434 0 -3428.5434 -2154.6422 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1020 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: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6895 ave 6895 max 6895 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: 120360 ave 120360 max 120360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120360 Ave neighs/atom = 118 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) = 5.132 | 5.132 | 5.132 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 -3428.5434 -3428.5434 46.032796 92.355389 4.0186819 -2154.6422 -2154.6422 4.6085169 -6466.4349 -2.1000861 2.6072574 419.72108 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1020 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: 1020 ave 1020 max 1020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6895 ave 6895 max 6895 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60180 ave 60180 max 60180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120360 ave 120360 max 120360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120360 Ave neighs/atom = 118 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.7500/numatoms.out 1020 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3428.5434241031-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3428.5434241031-1020*${isolated_atom_energy} variable adjusted_pe_metal equal -3428.5434241031-1020*0 print "${adjusted_pe_metal} eV" file output/dump_075.7500/energy.out -3428.5434241031 eV print "${mindist_metal} Angstroms" file output/dump_075.7500/mindistance.out 2.60725742611879 Angstroms write_dump all cfg output/dump_075.7500/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_075.7500/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06