LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  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 4.032988503575325*${_u_distance}
variable lattice_constant_converted equal 4.032988503575325*1
variable xmin_converted equal 0.0*${_u_distance}
variable xmin_converted equal 0.0*1
variable xmax_converted equal 61.030190445576196*${_u_distance}
variable xmax_converted equal 61.030190445576196*1
variable ymin_converted equal -61.03422343407977*${_u_distance}
variable ymin_converted equal -61.03422343407977*1
variable ymax_converted equal 61.03422343407977*${_u_distance}
variable ymax_converted equal 61.03422343407977*1
variable zmin_converted equal 0.0*${_u_distance}
variable zmin_converted equal 0.0*1
variable zmax_converted equal 4.032988503575325*${_u_distance}
variable zmax_converted equal 4.032988503575325*1
lattice            fcc ${lattice_constant_converted}
lattice            fcc 4.03298850357533
Lattice spacing in x,y,z = 4.03299 4.03299 4.03299
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 61.0301904455762 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 61.0301904455762 -61.0342234340798 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 61.0301904455762 -61.0342234340798 61.0342234340798 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 61.0301904455762 -61.0342234340798 61.0342234340798 0 ${zmax_converted} units box
region             whole block 0 61.0301904455762 -61.0342234340798 61.0342234340798 0 4.03298850357533 units box
create_box         2 whole
Created orthogonal box = (0 -61.0342 0) to (61.0302 61.0342 4.03299)
  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 61.0342234340798 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1
lattice            fcc 4.03298850357533 orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1
Lattice spacing in x,y,z = 4.53063 4.53063 4.03299
create_atoms       1 region upper
Created 918 atoms
  create_atoms CPU = 0.000241041 secs
group              upper type 1
918 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 6.8097356776897 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -61.0342234340798  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 15 2 0 orient y -2 15 0 orient z 0 0 1
lattice            fcc 4.03298850357533 orient x 15 2 0 orient y -2 15 0 orient z 0 0 1
Lattice spacing in x,y,z = 4.53063 4.53063 4.03299
create_atoms       2 region lower
Created 918 atoms
  create_atoms CPU = 0.000131845 secs
group              lower type 2
918 atoms in group lower
displace_atoms     lower move -6.8097356776897 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_u_mass}
mass               2 26.981538*1
pair_style         kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979)
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*4.03298850357533
delete_atoms       overlap ${delete_distance} all all
delete_atoms       overlap 2.01649425178767 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 = 13.7567
  ghost atom cutoff = 13.7567
  binsize = 6.87835, bins = 9 18 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 13.7567
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Deleted 26 atoms, new total = 1810
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 = 13.7567
  ghost atom cutoff = 13.7567
  binsize = 6.87835, bins = 9 18 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 13.7567
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.49 | 13.49 | 13.49 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -5223.5009            0   -5223.5009   -80.065388 
     381            0   -5262.0759            0   -5262.0759   -6419.3282 
Loop time of 18.3223 on 1 procs for 381 steps with 1810 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 = 
        -5223.50094969      -5262.0758562      -5262.0758562
  Force two-norm initial, final = 21.982 6.44061e-06
  Force max component initial, final = 4.35736 1.15745e-06
  Final line search alpha, max atom move = 1 1.15745e-06
  Iterations, force evaluations = 381 750

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 18.192     | 18.192     | 18.192     |   0.0 | 99.29
Neigh   | 0.018092   | 0.018092   | 0.018092   |   0.0 |  0.10
Comm    | 0.085222   | 0.085222   | 0.085222   |   0.0 |  0.47
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.02721    |            |       |  0.15

Nlocal:    1810 ave 1810 max 1810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23875 ave 23875 max 23875 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:  1.19974e+06 ave 1.19974e+06 max 1.19974e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1199744
Ave neighs/atom = 662.842
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) = 13.49 | 13.49 | 13.49 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     381            0   -5262.0759            0   -5262.0759   -6419.3282    30045.202 
    1381            0    -5262.482            0    -5262.482   -1458.9926    29841.829 
Loop time of 49.2736 on 1 procs for 1000 steps with 1810 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 = 
         -5262.0758562     -5262.48195867     -5262.48195868
  Force two-norm initial, final = 142.778 0.0182497
  Force max component initial, final = 115.313 0.0134559
  Final line search alpha, max atom move = 0.538102 0.00724062
  Iterations, force evaluations = 1000 1994

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 48.492     | 48.492     | 48.492     |   0.0 | 98.41
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21419    | 0.21419    | 0.21419    |   0.0 |  0.43
Output  | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.5676     |            |       |  1.15

Nlocal:    1810 ave 1810 max 1810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23927 ave 23927 max 23927 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:  1.19231e+06 ave 1.19231e+06 max 1.19231e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1192308
Ave neighs/atom = 658.734
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:52)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 13.7567
  ghost atom cutoff = 13.7567
  binsize = 6.87835, bins = 9 18 1
  3 neighbor lists, perpetual/occasional/extra = 1 2 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 13.7567
      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) = 13.01 | 13.01 | 13.01 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0    -5262.482            0    -5262.482   -1458.9926 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1810 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:    1810 ave 1810 max 1810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23982 ave 23982 max 23982 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:  1.19745e+06 ave 1.19745e+06 max 1.19745e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1197448
Ave neighs/atom = 661.573
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:52)
Per MPI rank memory allocation (min/avg/max) = 13.01 | 13.01 | 13.01 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    -5262.482    -5262.482    60.564683    122.06845    4.0364778   -1458.9926   -1458.9926  -0.59818643   -4375.6565   -0.7230556     2.489482    569.70743 
Loop time of 1.90735e-06 on 1 procs for 0 steps with 1810 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:    1810 ave 1810 max 1810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    23982 ave 23982 max 23982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    598724 ave 598724 max 598724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  1.19745e+06 ave 1.19745e+06 max 1.19745e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1197448
Ave neighs/atom = 661.573
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_015.1893/numatoms.out
1810
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -5262.48195867764-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -5262.48195867764-1810*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -5262.48195867764-1810*0
print              "${adjusted_pe_metal} eV" file output/dump_015.1893/energy.out
-5262.48195867764 eV
print              "${mindist_metal} Angstroms" file output/dump_015.1893/mindistance.out
2.48948195856803 Angstroms
write_dump         all cfg output/dump_015.1893/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_015.1893/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:01:07