LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
# input for unrelaxed vacancy formation energy at constant atomic volume

units           electron
atom_style      atomic

# Atomic volume for MGPT potential in a.u.
variable        atomic_vol equal 121.6

# Derive effective lattice volume from atomic volume for 249-site cell
variable        lat_vol equal ${atomic_vol}*249/250
variable        lat_vol equal 121.6*249/250

# Derive lattice constant from lattice volume
variable        lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable        lattice_constant equal (121.1136*2.0)^(1.0/3.0)

# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice         bcc ${lattice_constant}
lattice         bcc 6.23362926394575
Lattice spacing in x,y,z = 6.2336293 6.2336293 6.2336293
region          box block 0 5 0 5 0 5
create_box      1 box
Created orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 250 atoms
  using lattice units in orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
  create_atoms CPU = 0.000 seconds

# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249

# Define potential for use in simulation
pair_style      mgpt

# Set parameters for potential:
#                  parameter files  atomic volume
#pair_coeff      * * parmin potin    ${atomic_vol}
pair_coeff      * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin  ${atomic_vol}
pair_coeff      * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin  121.6
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30

# Create velocities at 0 K
velocity        all create 0.0 87287

# Set neighbor list parameters
neighbor        0.1 bin
neigh_modify    every 1 delay 0 check yes

# Set up microcanonical integrator
fix             1 all nve

# Dump coordinates to file every 50 timesteps
# dump            id all atom 50 dump.vac0-bcc

# Output thermodynamical data every 10 timesteps
thermo          10

# Set output quantities and output format
thermo_style custom step vol temp pe etotal press

## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e

# Run 0 timesteps
run             0
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 13.161827
  ghost atom cutoff = 13.161827
  binsize = 6.5809134, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair mgpt, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) pair mgpt, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes
   Step         Volume          Temp          PotEng         TotEng         Press     
         0   30278.4        0             -73.996387     -73.996387     -6.3426731e+08
Loop time of 1.016e-06 on 1 procs for 0 steps with 249 atoms

98.4% 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   |            | 1.016e-06  |            |       |100.00

Nlocal:            249 ave         249 max         249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1479 ave        1479 max        1479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           7936 ave        7936 max        7936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:        15872 ave       15872 max       15872 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 0
Dangerous builds = 0

# Convert energy to rydbergs and pressure to gpa

variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"

print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.6
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594348488796036
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -0.634267307139553
print "${natoms}   ${atvol}   ${etot}   ${ptotgpa}"
249   121.6   -147.992773710213   -0.634267307139553
print "${atvol}   ${etotry}   ${ptotgpa}"
121.6   -0.594348488796036   -0.634267307139553
Total wall time: 0:00:00
