345 lines
13 KiB
Groff
345 lines
13 KiB
Groff
LAMMPS (15 Apr 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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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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orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872)
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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 = 0.00148988 secs
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## EAM potential
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pair_style eam/fs
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pair_coeff * * Fe_mm.eam.fs Fe
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Reading potential file 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 9.17912e-06 on 4 procs for 0 steps with 687 atoms
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59.9% 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 | | 9.179e-06 | | |100.00
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Nlocal: 171.75 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 = 68.1849
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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 9.11951e-06 on 4 procs for 0 steps with 687 atoms
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52.1% 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 | | 9.12e-06 | | |100.00
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Nlocal: 171.75 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 = 68.1849
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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 0 com 1
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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 9.17912e-06 on 4 procs for 0 steps with 687 atoms
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84.4% 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 | | 9.179e-06 | | |100.00
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Nlocal: 171.75 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 = 68.1849
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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 (src/min.cpp:190)
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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 1.5010519e-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 5.028334e-14 -2828.3565 0 -2828.3565 3092.8883
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500 4.905696e-14 -2828.3565 0 -2828.3565 3092.8883
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600 4.8645524e-14 -2828.3565 0 -2828.3565 3092.8883
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700 4.8498896e-14 -2828.3565 0 -2828.3565 3092.8882
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800 4.8444558e-14 -2828.3565 0 -2828.3565 3092.8882
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900 4.8424652e-14 -2828.3565 0 -2828.3565 3092.8882
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1000 4.8416883e-14 -2828.3565 0 -2828.3565 3092.8882
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Loop time of 0.378521 on 4 procs for 1000 steps with 687 atoms
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94.6% CPU use with 4 MPI tasks x 1 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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-2828.24917967 -2828.35645844 -2828.35645844
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Force two-norm initial, final = 1.2831 7.46892e-07
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Force max component initial, final = 0.333171 2.93218e-07
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Final line search alpha, max atom move = 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 | 0.28507 | 0.30427 | 0.3132 | 2.1 | 80.38
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.041108 | 0.050675 | 0.070478 | 5.2 | 13.39
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Output | 0.00013185 | 0.00025684 | 0.00063133 | 0.0 | 0.07
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Modify | 0.012176 | 0.01298 | 0.013903 | 0.7 | 3.43
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Other | | 0.01034 | | | 2.73
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Nlocal: 171.75 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 = 68.1849
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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 4.8416883e-14 0
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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 0.358743 on 4 procs for 1000 steps with 687 atoms
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Performance: 240.841 ns/day, 0.100 hours/ns, 2787.512 timesteps/s
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97.5% 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 | 0.2806 | 0.29275 | 0.30044 | 1.4 | 81.60
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.028289 | 0.035765 | 0.047713 | 4.0 | 9.97
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Output | 0.00016427 | 0.00046188 | 0.001353 | 0.0 | 0.13
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Modify | 0.02722 | 0.027855 | 0.02832 | 0.2 | 7.76
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Other | | 0.001914 | | | 0.53
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Nlocal: 171.75 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 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 = 68.1863
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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 (src/min.cpp:190)
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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 5.8980022e-14 0.0018217607
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2400 -2828.3565 5.1597338e-14 0.0020531463
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2500 -2828.3565 4.9451625e-14 0.0022588465
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2600 -2828.3565 4.8775183e-14 0.0024468988
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2700 -2828.3565 4.8538712e-14 0.0026213819
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2800 -2828.3565 4.8450182e-14 0.0027849194
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2900 -2828.3565 4.8421015e-14 0.0029393609
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3000 -2828.3565 4.8409029e-14 0.0030860795
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Loop time of 0.358516 on 4 procs for 1000 steps with 687 atoms
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97.2% CPU use with 4 MPI tasks x 1 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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-2779.54493573 -2828.35646627 -2828.35646628
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Force two-norm initial, final = 29.3013 7.46923e-07
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Force max component initial, final = 2.07903 2.93237e-07
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Final line search alpha, max atom move = 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 | 0.28555 | 0.30143 | 0.30793 | 1.7 | 84.08
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.029324 | 0.035806 | 0.051662 | 4.9 | 9.99
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Output | 0.00016069 | 0.00043958 | 0.0012667 | 0.0 | 0.12
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Modify | 0.0087969 | 0.0089234 | 0.0090258 | 0.1 | 2.49
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Other | | 0.01192 | | | 3.32
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Nlocal: 171.75 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 = 70.786
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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 = ${adn} A,
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Average Force Projection Along MFEP = ${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 = 1.3664587498043e-05 A,
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Average Force Projection Along MFEP = -0.442220695378227 eV/A
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print """
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In-plane minimization post-run:
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energy = ${pe} eV
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"""
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In-plane minimization post-run:
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energy = -2828.3564662776 eV
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if "${maxjump} > 0.1" then "print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'"
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print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'
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Max Atomic Displacement = 0.00308607949101158A < 0.1A => No in-plane jumps
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print """
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----- END PAFI ----
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"""
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----- END PAFI ----
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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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#print """
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#Full minimization post-run:
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#energy = ${pe} eV
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#"""
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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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