402 lines
16 KiB
Groff
402 lines
16 KiB
Groff
LAMMPS (24 Aug 2020)
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units metal
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atom_style atomic
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atom_modify map array sort 0 0.0
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neigh_modify every 2 delay 10 check yes page 1000000 one 100000
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## read in path data using fix property/atom- here 4th image of a NEB
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fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
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read_data pafipath.4.data fix pa NULL PafiPath
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (19.987184 19.987184 19.987184)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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687 atoms
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read_data CPU = 0.007 seconds
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## EAM potential
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pair_style eam/fs
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pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
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Reading eam/fs potential file ../../../../potentials/Fe_mm.eam.fs with DATE: 2007-06-11
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mass * 55.85
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thermo 100
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min_style fire
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compute pe all pe
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variable pe equal pe
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run 0
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Neighbor list info ...
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update every 2 steps, delay 10 steps, check yes
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max neighbors/atom: 100000, page size: 1000000
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master list distance cutoff = 7.3
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ghost atom cutoff = 7.3
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binsize = 3.65, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eam/fs, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -2828.2492 0 -2828.2492 3015.2014
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Loop time of 6.88e-07 on 1 procs for 0 steps with 687 atoms
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290.7% CPU use with 1 MPI tasks x no 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 | | 6.88e-07 | | |100.00
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46843.0 ave 46843 max 46843 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46843
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Ave neighs/atom = 68.184862
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Neighbor list builds = 0
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Dangerous builds = 0
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print "energy=${pe}"
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energy=-2828.24917967199
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## compute property/atom to access relevant fields
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compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
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run 0
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Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -2828.2492 0 -2828.2492 3015.2014
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Loop time of 9.41e-07 on 1 procs for 0 steps with 687 atoms
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106.3% CPU use with 1 MPI tasks x no 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 | | 9.41e-07 | | |100.00
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46843.0 ave 46843 max 46843 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46843
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Ave neighs/atom = 68.184862
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Neighbor list builds = 0
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Dangerous builds = 0
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## fix name group-id pafi compute-id temperature tdamp seed overdamped 0/1 com 0/1
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fix hp all pafi pa 500.0 0.01 434 overdamped no com yes
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fix pafi compute name,style: pa,property/atom
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run 0
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Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -2828.2492 0 -2828.2492 3015.2014
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Loop time of 5.53002e-07 on 1 procs for 0 steps with 687 atoms
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361.7% CPU use with 1 MPI tasks x no 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 | | 5.53e-07 | | |100.00
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46843.0 ave 46843 max 46843 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46843
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Ave neighs/atom = 68.184862
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Neighbor list builds = 0
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Dangerous builds = 0
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minimize 0 0 1000 1000 # best if using NEB path
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
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Parameters for fire:
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dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
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0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
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Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -2828.2492 0 -2828.2492 3015.2014
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100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936
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200 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883
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300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883
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400 5.0283348e-14 -2828.3565 0 -2828.3565 3092.8883
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500 4.9056964e-14 -2828.3565 0 -2828.3565 3092.8883
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600 4.8645525e-14 -2828.3565 0 -2828.3565 3092.8883
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700 4.8498912e-14 -2828.3565 0 -2828.3565 3092.8882
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800 4.8444552e-14 -2828.3565 0 -2828.3565 3092.8882
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900 4.8424643e-14 -2828.3565 0 -2828.3565 3092.8882
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1000 4.84169e-14 -2828.3565 0 -2828.3565 3092.8882
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Loop time of 1.23105 on 1 procs for 1000 steps with 687 atoms
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-2828.24917967199 -2828.35645843665 -2828.35645844395
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Force two-norm initial, final = 1.2831004431533395 7.468917431980592e-07
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Force max component initial, final = 0.3331705829071986 2.93217567864934e-07
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Final line search alpha, max atom move = 0.0 0.0
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Iterations, force evaluations = 1000 1007
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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 | 1.1849 | 1.1849 | 1.1849 | 0.0 | 96.25
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.010743 | 0.010743 | 0.010743 | 0.0 | 0.87
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Output | 0.00013686 | 0.00013686 | 0.00013686 | 0.0 | 0.01
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Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 2.01
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Other | | 0.01055 | | | 0.86
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46843.0 ave 46843 max 46843 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46843
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Ave neighs/atom = 68.184862
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Neighbor list builds = 0
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Dangerous builds = 0
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compute dx all displace/atom
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compute dmag all reduce max c_dx[4]
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variable maxjump equal sqrt(c_dmag)
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thermo_style custom step pe temp v_maxjump
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variable dn equal f_hp[4]*f_hp[4] # should be zero to float precision
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fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
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variable adn equal sqrt(f_af[4]) # should be very small (approx. 1e-6 A)
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variable apf equal f_af[1]
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 8.778 | 8.778 | 8.778 Mbytes
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Step PotEng Temp v_maxjump
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1000 -2828.3565 4.84169e-14 3.9400009e-08
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1100 -2788.9297 505.16169 0.53846275
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1200 -2784.1274 471.52773 0.5820714
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1300 -2782.7071 503.23183 0.57990998
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1400 -2780.7259 531.16141 0.61955057
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1500 -2781.512 490.9404 0.58663715
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1600 -2783.4961 513.37777 0.65062082
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1700 -2780.0312 492.76259 0.5785296
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1800 -2781.6555 512.32986 0.58277945
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1900 -2782.1648 486.16736 0.58913114
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2000 -2781.1942 493.15046 0.56962281
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Loop time of 1.3463 on 1 procs for 1000 steps with 687 atoms
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Performance: 64.176 ns/day, 0.374 hours/ns, 742.778 timesteps/s
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100.0% CPU use with 1 MPI tasks x no 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 | 1.2429 | 1.2429 | 1.2429 | 0.0 | 92.32
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.011341 | 0.011341 | 0.011341 | 0.0 | 0.84
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Output | 0.0001418 | 0.0001418 | 0.0001418 | 0.0 | 0.01
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Modify | 0.089655 | 0.089655 | 0.089655 | 0.0 | 6.66
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Other | | 0.002248 | | | 0.17
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46844.0 ave 46844 max 46844 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46844
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Ave neighs/atom = 68.186317
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Neighbor list builds = 0
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Dangerous builds = 0
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minimize 0 0 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
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Parameters for fire:
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dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
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0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
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Per MPI rank memory allocation (min/avg/max) = 9.278 | 9.278 | 9.278 Mbytes
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Step PotEng Temp v_maxjump
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2000 -2781.1942 0 0.56962281
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2100 -2828.3564 2.3533517e-06 0.028829312
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2200 -2828.3565 2.3166114e-09 0.0015098779
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2300 -2828.3565 5.7159208e-14 0.0017926087
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2400 -2828.3565 5.0928429e-14 0.0020264648
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2500 -2828.3565 4.9253427e-14 0.0022344754
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2600 -2828.3565 4.8706717e-14 0.0024243813
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2700 -2828.3565 4.8513392e-14 0.0026003645
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2800 -2828.3565 4.8442915e-14 0.0027651416
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2900 -2828.3565 4.8417422e-14 0.0029206277
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3000 -2828.3565 4.840734e-14 0.0030682417
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Loop time of 1.24896 on 1 procs for 1000 steps with 687 atoms
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-2781.19422468903 -2828.35646618005 -2828.35646618733
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Force two-norm initial, final = 29.0662462838641 7.469228601686482e-07
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Force max component initial, final = 2.2910705425983147 2.932332034966123e-07
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Final line search alpha, max atom move = 0.0 0.0
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Iterations, force evaluations = 1000 1008
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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 | 1.2027 | 1.2027 | 1.2027 | 0.0 | 96.30
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.010706 | 0.010706 | 0.010706 | 0.0 | 0.86
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Output | 0.00016364 | 0.00016364 | 0.00016364 | 0.0 | 0.01
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Modify | 0.024873 | 0.024873 | 0.024873 | 0.0 | 1.99
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Other | | 0.01053 | | | 0.84
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3209.00 ave 3209 max 3209 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 48576.0 ave 48576 max 48576 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 48576
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Ave neighs/atom = 70.707424
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Neighbor list builds = 0
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Dangerous builds = 0
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variable s_pe equal ${pe}
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variable s_pe equal -2828.35646618733
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variable s_apf equal ${apf}
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variable s_apf equal -0.117797263023891
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variable s_adn equal ${adn}
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variable s_adn equal 1.36645874805011e-05
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variable s_maxjump equal ${maxjump}
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variable s_maxjump equal 0.00306824174470598
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unfix hp
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unfix pa
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unfix af
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minimize 0 0 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
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Parameters for fire:
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dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
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0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
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Per MPI rank memory allocation (min/avg/max) = 8.778 | 8.778 | 8.778 Mbytes
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Step PotEng Temp v_maxjump
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3000 -2828.3565 0 0.0030682417
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3100 -2828.5793 0.00016081731 0.54349309
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3200 -2828.5793 1.1620454e-14 0.54386121
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3300 -2828.5793 4.4699993e-19 0.54386124
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3400 -2828.5793 1.0681196e-23 0.54386124
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3500 -2828.5793 2.046642e-25 0.54386124
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3600 -2828.5793 1.4539039e-25 0.54386124
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3700 -2828.5793 2.0152508e-25 0.54386124
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3800 -2828.5793 1.3593174e-25 0.54386124
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3900 -2828.5793 1.8155665e-25 0.54386124
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4000 -2828.5793 1.2308872e-25 0.54386124
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Loop time of 1.20543 on 1 procs for 1000 steps with 687 atoms
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-2828.35646618733 -2828.57925588226 -2828.57925588226
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Force two-norm initial, final = 0.5639141583763609 2.3523921777846766e-13
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Force max component initial, final = 0.22089321768110187 2.037953139577553e-14
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Final line search alpha, max atom move = 0.0 0.0
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Iterations, force evaluations = 1000 1017
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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 | 1.1843 | 1.1843 | 1.1843 | 0.0 | 98.25
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.010469 | 0.010469 | 0.010469 | 0.0 | 0.87
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Output | 0.00012213 | 0.00012213 | 0.00012213 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01051 | | | 0.87
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Nlocal: 687.000 ave 687 max 687 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3239.00 ave 3239 max 3239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46844.0 ave 46844 max 46844 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46844
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Ave neighs/atom = 68.186317
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Neighbor list builds = 0
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Dangerous builds = 0
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print """
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---------- PAFI RESULTS --------
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During run:
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Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
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Average Force Projection Along MFEP = ${s_apf} eV/A
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"""
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---------- PAFI RESULTS --------
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During run:
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Average Distance From Hyperplane = 1.36645874805011e-05A (Should be very small, around 1e-5A),
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Average Force Projection Along MFEP = -0.117797263023891 eV/A
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print """
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In-plane minimization post-run:
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energy = ${s_pe} eV
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"""
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In-plane minimization post-run:
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energy = -2828.35646618733 eV
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if "${s_maxjump} > 0.1" then "print 'Max Atomic Displacement = ${s_maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"
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print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'
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Max Atomic Displacement = 0.00306824174470598A < 0.1A => No in-plane jumps
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print """
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Full minimization after removal of PAFI fixes:
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energy = ${pe} eV
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----- END PAFI ----
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"""
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Full minimization after removal of PAFI fixes:
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energy = -2828.57925588226 eV
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----- END PAFI ----
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:05
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