135 lines
4.8 KiB
Groff
135 lines
4.8 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 in bulk bcc structure
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units electron
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atom_style atomic
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# Atomic volume for MGPT potential in a.u.
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variable atomic_vol equal 121.6
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# Derive lattice constant from volume
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variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
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variable lattice_constant equal (121.6*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 6.24196300283154
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Lattice spacing in x,y,z = 6.241963 6.241963 6.241963
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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 (31.209815 31.209815 31.209815)
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1 by 2 by 2 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 (31.209815 31.209815 31.209815)
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create_atoms CPU = 0.000 seconds
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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 121.6
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Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
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# Create velocities at 0 K
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velocity all create 0.0 87287
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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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# Set up microcanonical integrator
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fix 1 all nve
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# Dump coordinates to file every 50 timesteps
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#dump id all atom 50 dump.bcc0
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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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# Run 0 timesteps
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run 0
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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 = 13.161827
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ghost atom cutoff = 13.161827
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binsize = 6.5809134, 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) = 3.73 | 3.73 | 3.73 Mbytes
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Step Volume Temp PotEng TotEng Press
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0 30400 0 -74.412503 -74.412503 -1.1594626e+09
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Loop time of 3.56525e-06 on 4 procs for 0 steps with 250 atoms
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119.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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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 | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 3.565e-06 | | |100.00
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Nlocal: 62.5 ave 65 max 60 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 868.5 ave 871 max 866 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 2000 ave 2110 max 1890 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 4000 ave 4160 max 3840 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 16000
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Ave neighs/atom = 64
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Neighbor list builds = 0
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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 = 250
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print "atomic volume (a.u.) = ${atvol}"
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atomic volume (a.u.) = 121.6
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print "total energy (ry/atom) = ${etotry}"
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total energy (ry/atom) = -0.595300024887348
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print "pressure (gpa) = ${ptotgpa}"
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pressure (gpa) = -1.15946260887575
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print "${natoms} ${atvol} ${etot} ${ptotgpa}"
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250 121.6 -148.825006221837 -1.15946260887575
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print "${atvol} ${etotry} ${ptotgpa}"
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121.6 -0.595300024887348 -1.15946260887575
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Total wall time: 0:00:00
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