163 lines
6.7 KiB
Groff
163 lines
6.7 KiB
Groff
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
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# input for relaxed vacancy formation energy at constant pressure
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units electron
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atom_style atomic
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# Atomic volume for MGPT potential
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variable atomic_vol equal 121.863
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# Derive effective lattice volume from atomic volume for 249-site cell
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variable lat_vol equal ${atomic_vol}*249/250
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variable lat_vol equal 121.863*249/250
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# Derive lattice constant from lattice volume
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variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
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variable lattice_constant equal (121.375548*2.0)^(1.0/3.0)
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# Create bcc lattice with 5x5x5 unit cells (250 atoms)
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lattice bcc ${lattice_constant}
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lattice bcc 6.23812011912273
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Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 250 atoms
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using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
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create_atoms CPU = 0.000 seconds
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# Remove central atom from bcc lattice to create vacancy
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region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
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delete_atoms region vacancy
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Deleted 1 atoms, new total = 249
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# Define potential for use in simulation
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pair_style mgpt
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# Set parameters for potential:
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# parameter files atomic volume
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#pair_coeff * * parmin potin ${atomic_vol}
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pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
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pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863
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Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
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# Set neighbor list parameters
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neighbor 0.1 bin
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neigh_modify every 1 delay 0 check yes
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# Dump coordinates to file every 50 timesteps
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# dump id all atom 50 dump.vacmin-bcc
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# Output thermodynamical data every 10 timesteps
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thermo 10
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# Set output quantities and output format
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thermo_style custom step vol temp pe etotal press
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## Example: Output floating point number with 5 digits exponential notation.
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#thermo_modify format float %15.5e
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# minimize total energy
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min_style cg
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minimize 1.0e-10 1.0e-10 5000 10000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13.171237
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ghost atom cutoff = 13.171237
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binsize = 6.5856184, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair mgpt, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) pair mgpt, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.88 | 4.88 | 4.88 Mbytes
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Step Volume Temp PotEng TotEng Press
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0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
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10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
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20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
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30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
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40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
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50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
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60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
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70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
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80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
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90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
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100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
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110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
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120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
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130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
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139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
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Loop time of 2.58636 on 1 procs for 139 steps with 249 atoms
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90.5% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-73.9945109564338 -74.0063705487283 -74.0063705557007
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Force two-norm initial, final = 0.036622686 8.090814e-05
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Force max component initial, final = 0.0073094815 8.0524205e-06
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Final line search alpha, max atom move = 1 8.0524205e-06
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Iterations, force evaluations = 139 139
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.5671 | 2.5671 | 2.5671 | 0.0 | 99.26
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Neigh | 0.015241 | 0.015241 | 0.015241 | 0.0 | 0.59
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Comm | 0.001446 | 0.001446 | 0.001446 | 0.0 | 0.06
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Output | 0.00038428 | 0.00038428 | 0.00038428 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.002161 | | | 0.08
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Nlocal: 249 ave 249 max 249 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1479 ave 1479 max 1479 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7936 ave 7936 max 7936 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 15872 ave 15872 max 15872 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15872
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Ave neighs/atom = 63.742972
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Neighbor list builds = 4
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Dangerous builds = 0
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# Convert energy to rydbergs and pressure to gpa
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variable natoms equal "count(all)"
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variable voltot equal "vol"
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variable atvol equal "v_voltot/v_natoms"
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variable etot equal "2.0*pe"
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variable etotry equal "v_etot/v_natoms"
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variable ptot equal "press"
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variable ptotgpa equal "v_ptot/1.0e+09"
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print "number of atoms = ${natoms}"
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number of atoms = 249
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print "atomic volume (a.u.) = ${atvol}"
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atomic volume (a.u.) = 121.863
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print "total energy (ry/atom) = ${etotry}"
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total energy (ry/atom) = -0.594428679162253
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print "pressure (gpa) = ${ptotgpa}"
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pressure (gpa) = -1.15783109516516
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print "${natoms} ${atvol} ${etot} ${ptotgpa}"
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249 121.863 -148.012741111401 -1.15783109516516
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print "${atvol} ${etotry} ${ptotgpa}"
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121.863 -0.594428679162253 -1.15783109516516
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Total wall time: 0:00:02
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