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