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 3.9946166351437573*${_u_distance}
variable lattice_constant_converted equal 3.9946166351437573*1
variable xmin_converted equal 0.0*${_u_distance}
variable xmin_converted equal 0.0*1
variable xmax_converted equal 46.755788972726265*${_u_distance}
variable xmax_converted equal 46.755788972726265*1
variable ymin_converted equal -46.75978358936141*${_u_distance}
variable ymin_converted equal -46.75978358936141*1
variable ymax_converted equal 46.75978358936141*${_u_distance}
variable ymax_converted equal 46.75978358936141*1
variable zmin_converted equal 0.0*${_u_distance}
variable zmin_converted equal 0.0*1
variable zmax_converted equal 3.9946166351437573*${_u_distance}
variable zmax_converted equal 3.9946166351437573*1
lattice            fcc ${lattice_constant_converted}
lattice            fcc 3.99461663514376
Lattice spacing in x,y,z = 3.99462 3.99462 3.99462
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 46.7557889727263 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 46.7557889727263 -46.7597835893614 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 46.7557889727263 -46.7597835893614 46.7597835893614 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 46.7557889727263 -46.7597835893614 46.7597835893614 0 ${zmax_converted} units box
region             whole block 0 46.7557889727263 -46.7597835893614 46.7597835893614 0 3.99461663514376 units box
create_box         2 whole
Created orthogonal box = (0 -46.7598 0) to (46.7558 46.7598 3.99462)
  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 46.7597835893614 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1
lattice            fcc 3.99461663514376 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.11925 5.11925 3.99462
create_atoms       1 region upper
Created 550 atoms
  create_atoms CPU = 0.00022006 secs
group              upper type 1
550 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 5.267114959823831 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -46.7597835893614  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1
lattice            fcc 3.99461663514376 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.11925 5.11925 3.99462
create_atoms       2 region lower
Created 550 atoms
  create_atoms CPU = 9.10759e-05 secs
group              lower type 2
550 atoms in group lower
displace_atoms     lower move -5.267114959823831 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_u_mass}
mass               2 26.981538*1
pair_style         kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001
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*3.99461663514376
delete_atoms       overlap ${delete_distance} all all
delete_atoms       overlap 1.99730831757188 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 = 7.61876
  ghost atom cutoff = 7.61876
  binsize = 3.80938, 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 7.61876
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Deleted 26 atoms, new total = 1074
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 = 7.61876
  ghost atom cutoff = 7.61876
  binsize = 3.80938, bins = 13 25 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7.61876
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.008 | 5.008 | 5.008 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3504.1663            0   -3504.1663   -229.02208 
     107            0   -3514.5978            0   -3514.5978   -5310.9759 
Loop time of 1.21737 on 1 procs for 107 steps with 1074 atoms

100.2% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -3504.16628771     -3514.59779901     -3514.59779901
  Force two-norm initial, final = 8.70288 0.0134181
  Force max component initial, final = 2.53305 0.00275506
  Final line search alpha, max atom move = 6.10352e-05 1.68155e-07
  Iterations, force evaluations = 107 220

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2021     | 1.2021     | 1.2021     |   0.0 | 98.75
Neigh   | 0.0025949  | 0.0025949  | 0.0025949  |   0.0 |  0.21
Comm    | 0.0080245  | 0.0080245  | 0.0080245  |   0.0 |  0.66
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.004658   |            |       |  0.38

Nlocal:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7159 ave 7159 max 7159 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:  138892 ave 138892 max 138892 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 138892
Ave neighs/atom = 129.322
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) = 5.008 | 5.008 | 5.008 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     107            0   -3514.5978            0   -3514.5978   -5310.9759    17466.785 
     116            0   -3514.8519            0   -3514.8519   -1367.4635    17287.839 
Loop time of 0.331326 on 1 procs for 9 steps with 1074 atoms

99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -3514.59779901     -3514.85187126     -3514.85187126
  Force two-norm initial, final = 69.2119 1.35738
  Force max component initial, final = 51.5812 1.02811
  Final line search alpha, max atom move = 4.30238e-09 4.42331e-09
  Iterations, force evaluations = 9 48

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.32449    | 0.32449    | 0.32449    |   0.0 | 97.94
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0016537  | 0.0016537  | 0.0016537  |   0.0 |  0.50
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.005179   |            |       |  1.56

Nlocal:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    6813 ave 6813 max 6813 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:  139016 ave 139016 max 139016 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 139016
Ave neighs/atom = 129.438
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 -6.30324000329931e-20
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 = 7.61876
  ghost atom cutoff = 7.61876
  binsize = 3.80938, bins = 13 25 2
  3 neighbor lists, perpetual/occasional/extra = 1 2 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7.61876
      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) = 5.144 | 5.144 | 5.144 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3514.8519            0   -3514.8519   -1367.4635 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    6851 ave 6851 max 6851 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:  139852 ave 139852 max 139852 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 139852
Ave neighs/atom = 130.216
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) = 5.144 | 5.144 | 5.144 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   -3514.8519   -3514.8519    46.525117    93.519567    3.9732943   -1367.4635   -1367.4635    81.567469    -4278.731    94.772926    2.5140732    777.27959 
Loop time of 1.90735e-06 on 1 procs for 0 steps with 1074 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:    1074 ave 1074 max 1074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    6851 ave 6851 max 6851 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    69926 ave 69926 max 69926 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  139852 ave 139852 max 139852 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 139852
Ave neighs/atom = 130.216
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_039.9662/numatoms.out
1074
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3514.85187126195-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3514.85187126195-1074*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3514.85187126195-1074*-6.30324000329931e-20
print              "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out
-3514.85187126195 eV
print              "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out
2.51407323932513 Angstroms
write_dump         all cfg output/dump_039.9662/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_039.9662/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:00:01