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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2 by 1 by 2 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) = 6.844 | 6.844 | 6.844 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 2.82e-06 on 4 procs for 0 steps with 687 atoms
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97.5% CPU use with 4 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 | | 2.82e-06 | | |100.00
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Nlocal: 171.750 ave 187 max 163 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 1854.25 ave 1863 max 1839 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 11710.8 ave 12319 max 10647 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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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=-2828.24917967201
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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) = 6.844 | 6.844 | 6.844 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 2.667e-06 on 4 procs for 0 steps with 687 atoms
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37.5% CPU use with 4 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 | | 2.667e-06 | | |100.00
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Nlocal: 171.750 ave 187 max 163 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 1854.25 ave 1863 max 1839 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 11710.8 ave 12319 max 10647 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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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) = 8.344 | 8.344 | 8.344 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 2.52725e-06 on 4 procs for 0 steps with 687 atoms
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108.8% CPU use with 4 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 | | 2.527e-06 | | |100.00
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Nlocal: 171.750 ave 187 max 163 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 1854.25 ave 1863 max 1839 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 11710.8 ave 12319 max 10647 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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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) = 8.344 | 8.344 | 8.344 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 1.501052e-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 5.0283344e-14 -2828.3565 0 -2828.3565 3092.8883
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500 4.9056968e-14 -2828.3565 0 -2828.3565 3092.8883
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600 4.8645528e-14 -2828.3565 0 -2828.3565 3092.8883
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700 4.8498892e-14 -2828.3565 0 -2828.3565 3092.8882
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800 4.8444568e-14 -2828.3565 0 -2828.3565 3092.8882
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900 4.8424653e-14 -2828.3565 0 -2828.3565 3092.8882
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1000 4.8416878e-14 -2828.3565 0 -2828.3565 3092.8882
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Loop time of 0.43333 on 4 procs for 1000 steps with 687 atoms
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95.4% CPU use with 4 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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-2828.24917967201 -2828.35645843663 -2828.3564584439
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Force two-norm initial, final = 1.2831004431533406 7.468917439994878e-07
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Force max component initial, final = 0.33317058290719853 2.9321733663323357e-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 | 0.3303 | 0.34246 | 0.35813 | 1.7 | 79.03
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.046971 | 0.062117 | 0.073961 | 3.9 | 14.33
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Output | 0.00013746 | 0.00014874 | 0.00016997 | 0.0 | 0.03
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Modify | 0.0099064 | 0.01077 | 0.011612 | 0.6 | 2.49
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Other | | 0.01784 | | | 4.12
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Nlocal: 171.750 ave 187 max 163 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 1854.25 ave 1863 max 1839 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 11710.8 ave 12319 max 10647 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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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) = 8.719 | 8.719 | 8.719 Mbytes
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Step PotEng Temp v_maxjump
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1000 -2828.3565 4.8416878e-14 3.9625012e-08
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1100 -2787.3877 503.1749 0.53858794
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1200 -2783.8463 508.91879 0.57609619
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1300 -2782.5288 533.03961 0.64090828
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1400 -2782.4551 508.05688 0.61706248
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1500 -2784.0499 538.34202 0.56379358
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1600 -2786.4068 487.9633 0.57600511
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1700 -2780.7727 489.2309 0.61048418
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1800 -2780.4909 519.01911 0.60204913
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1900 -2782.0825 512.3441 0.6071772
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2000 -2779.5449 526.21838 0.58247597
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Loop time of 0.446418 on 4 procs for 1000 steps with 687 atoms
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Performance: 193.541 ns/day, 0.124 hours/ns, 2240.053 timesteps/s
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95.8% CPU use with 4 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 | 0.34383 | 0.35018 | 0.35655 | 0.9 | 78.44
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.049244 | 0.055398 | 0.061404 | 2.2 | 12.41
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Output | 0.00015376 | 0.00016326 | 0.00018954 | 0.0 | 0.04
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Modify | 0.034111 | 0.034443 | 0.03473 | 0.1 | 7.72
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Other | | 0.006229 | | | 1.40
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Nlocal: 171.750 ave 183 max 165 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 1854.25 ave 1861 max 1843 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Neighs: 11711.0 ave 12115 max 10983 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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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) = 9.219 | 9.219 | 9.219 Mbytes
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Step PotEng Temp v_maxjump
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2000 -2779.5449 0 0.58247597
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2100 -2828.3564 5.5901288e-06 0.022258122
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2200 -2828.3565 2.5724945e-11 0.0014462408
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2300 -2828.3565 5.8980018e-14 0.0018217607
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2400 -2828.3565 5.1597335e-14 0.0020531463
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2500 -2828.3565 4.9451623e-14 0.0022588465
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2600 -2828.3565 4.8775183e-14 0.0024468988
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2700 -2828.3565 4.8538707e-14 0.0026213819
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2800 -2828.3565 4.8450209e-14 0.0027849194
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2900 -2828.3565 4.8421002e-14 0.0029393609
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3000 -2828.3565 4.8409037e-14 0.0030860795
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Loop time of 0.432206 on 4 procs for 1000 steps with 687 atoms
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91.9% CPU use with 4 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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-2779.54493572831 -2828.35646627033 -2828.3564662776
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Force two-norm initial, final = 29.30132707276523 7.469232246845132e-07
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Force max component initial, final = 2.0790292865239595 2.9323707292916446e-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 | 0.33828 | 0.34752 | 0.35566 | 1.1 | 80.41
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.04768 | 0.056242 | 0.065447 | 2.8 | 13.01
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Output | 0.00016892 | 0.00018009 | 0.00020427 | 0.0 | 0.04
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Modify | 0.010016 | 0.010698 | 0.011316 | 0.4 | 2.48
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Other | | 0.01756 | | | 4.06
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Nlocal: 171.750 ave 184 max 165 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Nghost: 1828.25 ave 1835 max 1815 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Neighs: 12157.5 ave 12578 max 11155 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Total # of neighbors = 48630
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Ave neighs/atom = 70.786026
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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 -2828.3564662776
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variable s_apf equal ${apf}
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variable s_apf equal -0.44222069537824
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variable s_adn equal ${adn}
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variable s_adn equal 1.36645875188617e-05
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variable s_maxjump equal ${maxjump}
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variable s_maxjump equal 0.00308607949485962
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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) = 8.719 | 8.719 | 8.719 Mbytes
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Step PotEng Temp v_maxjump
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3000 -2828.3565 0 0.0030860795
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3100 -2828.5793 0.00016081696 0.5434931
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3200 -2828.5793 1.1620338e-14 0.54386121
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3300 -2828.5793 4.4708247e-19 0.54386124
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3400 -2828.5793 1.0642423e-23 0.54386124
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3500 -2828.5793 1.9858026e-25 0.54386124
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3600 -2828.5793 1.395464e-25 0.54386124
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3700 -2828.5793 2.0687121e-25 0.54386124
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3800 -2828.5793 1.3586688e-25 0.54386124
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3900 -2828.5793 2.0485828e-25 0.54386124
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4000 -2828.5793 1.3803592e-25 0.54386124
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Loop time of 0.427843 on 4 procs for 1000 steps with 687 atoms
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96.5% CPU use with 4 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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-2828.3564662776 -2828.57925588218 -2828.57925588218
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Force two-norm initial, final = 0.5639144322930092 2.34573110665124e-13
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Force max component initial, final = 0.22089332498188619 2.0969337377607644e-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 | 0.34748 | 0.35476 | 0.3611 | 0.9 | 82.92
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.049149 | 0.054906 | 0.062132 | 2.2 | 12.83
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Output | 0.00015435 | 0.00016534 | 0.00018687 | 0.0 | 0.04
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01801 | | | 4.21
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Nlocal: 171.750 ave 183 max 165 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 1854.25 ave 1861 max 1843 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Neighs: 11711.0 ave 12115 max 10983 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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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 = 1.36645875188617e-05A (Should be very small, around 1e-5A),
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Average Force Projection Along MFEP = -0.44222069537824 eV/A
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print """
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In-plane minimization post-run:
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energy = ${s_pe} eV
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"""
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In-plane minimization post-run:
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energy = -2828.3564662776 eV
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if "${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 = 0.00308607949485962A < 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 = -2828.57925588218 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: 0:00:01
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