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) 2 by 1 by 2 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) = 6.844 | 6.844 | 6.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2828.2492 0 -2828.2492 3015.2014 Loop time of 2.82e-06 on 4 procs for 0 steps with 687 atoms 97.5% CPU use with 4 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 | | 2.82e-06 | | |100.00 Nlocal: 171.750 ave 187 max 163 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 1854.25 ave 1863 max 1839 min Histogram: 1 0 0 0 0 0 0 1 1 1 Neighs: 11710.8 ave 12319 max 10647 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 46843 Ave neighs/atom = 68.184862 Neighbor list builds = 0 Dangerous builds = 0 print "energy=${pe}" energy=-2828.24917967201 ## 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) = 6.844 | 6.844 | 6.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2828.2492 0 -2828.2492 3015.2014 Loop time of 2.667e-06 on 4 procs for 0 steps with 687 atoms 37.5% CPU use with 4 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 | | 2.667e-06 | | |100.00 Nlocal: 171.750 ave 187 max 163 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 1854.25 ave 1863 max 1839 min Histogram: 1 0 0 0 0 0 0 1 1 1 Neighs: 11710.8 ave 12319 max 10647 min Histogram: 1 0 0 0 0 0 0 1 1 1 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) = 8.344 | 8.344 | 8.344 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2828.2492 0 -2828.2492 3015.2014 Loop time of 2.52725e-06 on 4 procs for 0 steps with 687 atoms 108.8% CPU use with 4 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 | | 2.527e-06 | | |100.00 Nlocal: 171.750 ave 187 max 163 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 1854.25 ave 1863 max 1839 min Histogram: 1 0 0 0 0 0 0 1 1 1 Neighs: 11710.8 ave 12319 max 10647 min Histogram: 1 0 0 0 0 0 0 1 1 1 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) = 8.344 | 8.344 | 8.344 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 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883 300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883 400 5.0283344e-14 -2828.3565 0 -2828.3565 3092.8883 500 4.9056968e-14 -2828.3565 0 -2828.3565 3092.8883 600 4.8645528e-14 -2828.3565 0 -2828.3565 3092.8883 700 4.8498892e-14 -2828.3565 0 -2828.3565 3092.8882 800 4.8444568e-14 -2828.3565 0 -2828.3565 3092.8882 900 4.8424653e-14 -2828.3565 0 -2828.3565 3092.8882 1000 4.8416878e-14 -2828.3565 0 -2828.3565 3092.8882 Loop time of 0.43333 on 4 procs for 1000 steps with 687 atoms 95.4% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2828.24917967201 -2828.35645843663 -2828.3564584439 Force two-norm initial, final = 1.2831004431533406 7.468917439994878e-07 Force max component initial, final = 0.33317058290719853 2.9321733663323357e-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 | 0.3303 | 0.34246 | 0.35813 | 1.7 | 79.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.046971 | 0.062117 | 0.073961 | 3.9 | 14.33 Output | 0.00013746 | 0.00014874 | 0.00016997 | 0.0 | 0.03 Modify | 0.0099064 | 0.01077 | 0.011612 | 0.6 | 2.49 Other | | 0.01784 | | | 4.12 Nlocal: 171.750 ave 187 max 163 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 1854.25 ave 1863 max 1839 min Histogram: 1 0 0 0 0 0 0 1 1 1 Neighs: 11710.8 ave 12319 max 10647 min Histogram: 1 0 0 0 0 0 0 1 1 1 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) = 8.719 | 8.719 | 8.719 Mbytes Step PotEng Temp v_maxjump 1000 -2828.3565 4.8416878e-14 3.9625012e-08 1100 -2787.3877 503.1749 0.53858794 1200 -2783.8463 508.91879 0.57609619 1300 -2782.5288 533.03961 0.64090828 1400 -2782.4551 508.05688 0.61706248 1500 -2784.0499 538.34202 0.56379358 1600 -2786.4068 487.9633 0.57600511 1700 -2780.7727 489.2309 0.61048418 1800 -2780.4909 519.01911 0.60204913 1900 -2782.0825 512.3441 0.6071772 2000 -2779.5449 526.21838 0.58247597 Loop time of 0.446418 on 4 procs for 1000 steps with 687 atoms Performance: 193.541 ns/day, 0.124 hours/ns, 2240.053 timesteps/s 95.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34383 | 0.35018 | 0.35655 | 0.9 | 78.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.049244 | 0.055398 | 0.061404 | 2.2 | 12.41 Output | 0.00015376 | 0.00016326 | 0.00018954 | 0.0 | 0.04 Modify | 0.034111 | 0.034443 | 0.03473 | 0.1 | 7.72 Other | | 0.006229 | | | 1.40 Nlocal: 171.750 ave 183 max 165 min Histogram: 1 1 0 1 0 0 0 0 0 1 Nghost: 1854.25 ave 1861 max 1843 min Histogram: 1 0 0 0 0 0 1 0 1 1 Neighs: 11711.0 ave 12115 max 10983 min Histogram: 1 0 0 0 0 0 1 0 1 1 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) = 9.219 | 9.219 | 9.219 Mbytes Step PotEng Temp v_maxjump 2000 -2779.5449 0 0.58247597 2100 -2828.3564 5.5901288e-06 0.022258122 2200 -2828.3565 2.5724945e-11 0.0014462408 2300 -2828.3565 5.8980018e-14 0.0018217607 2400 -2828.3565 5.1597335e-14 0.0020531463 2500 -2828.3565 4.9451623e-14 0.0022588465 2600 -2828.3565 4.8775183e-14 0.0024468988 2700 -2828.3565 4.8538707e-14 0.0026213819 2800 -2828.3565 4.8450209e-14 0.0027849194 2900 -2828.3565 4.8421002e-14 0.0029393609 3000 -2828.3565 4.8409037e-14 0.0030860795 Loop time of 0.432206 on 4 procs for 1000 steps with 687 atoms 91.9% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2779.54493572831 -2828.35646627033 -2828.3564662776 Force two-norm initial, final = 29.30132707276523 7.469232246845132e-07 Force max component initial, final = 2.0790292865239595 2.9323707292916446e-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 | 0.33828 | 0.34752 | 0.35566 | 1.1 | 80.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04768 | 0.056242 | 0.065447 | 2.8 | 13.01 Output | 0.00016892 | 0.00018009 | 0.00020427 | 0.0 | 0.04 Modify | 0.010016 | 0.010698 | 0.011316 | 0.4 | 2.48 Other | | 0.01756 | | | 4.06 Nlocal: 171.750 ave 184 max 165 min Histogram: 1 0 2 0 0 0 0 0 0 1 Nghost: 1828.25 ave 1835 max 1815 min Histogram: 1 0 0 0 0 0 0 1 0 2 Neighs: 12157.5 ave 12578 max 11155 min Histogram: 1 0 0 0 0 0 0 0 0 3 Total # of neighbors = 48630 Ave neighs/atom = 70.786026 Neighbor list builds = 0 Dangerous builds = 0 variable s_pe equal ${pe} variable s_pe equal -2828.3564662776 variable s_apf equal ${apf} variable s_apf equal -0.44222069537824 variable s_adn equal ${adn} variable s_adn equal 1.36645875188617e-05 variable s_maxjump equal ${maxjump} variable s_maxjump equal 0.00308607949485962 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) = 8.719 | 8.719 | 8.719 Mbytes Step PotEng Temp v_maxjump 3000 -2828.3565 0 0.0030860795 3100 -2828.5793 0.00016081696 0.5434931 3200 -2828.5793 1.1620338e-14 0.54386121 3300 -2828.5793 4.4708247e-19 0.54386124 3400 -2828.5793 1.0642423e-23 0.54386124 3500 -2828.5793 1.9858026e-25 0.54386124 3600 -2828.5793 1.395464e-25 0.54386124 3700 -2828.5793 2.0687121e-25 0.54386124 3800 -2828.5793 1.3586688e-25 0.54386124 3900 -2828.5793 2.0485828e-25 0.54386124 4000 -2828.5793 1.3803592e-25 0.54386124 Loop time of 0.427843 on 4 procs for 1000 steps with 687 atoms 96.5% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2828.3564662776 -2828.57925588218 -2828.57925588218 Force two-norm initial, final = 0.5639144322930092 2.34573110665124e-13 Force max component initial, final = 0.22089332498188619 2.0969337377607644e-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 | 0.34748 | 0.35476 | 0.3611 | 0.9 | 82.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.049149 | 0.054906 | 0.062132 | 2.2 | 12.83 Output | 0.00015435 | 0.00016534 | 0.00018687 | 0.0 | 0.04 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01801 | | | 4.21 Nlocal: 171.750 ave 183 max 165 min Histogram: 1 1 0 1 0 0 0 0 0 1 Nghost: 1854.25 ave 1861 max 1843 min Histogram: 1 0 0 0 0 0 1 0 1 1 Neighs: 11711.0 ave 12115 max 10983 min Histogram: 1 0 0 0 0 0 1 0 1 1 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 = 1.36645875188617e-05A (Should be very small, around 1e-5A), Average Force Projection Along MFEP = -0.44222069537824 eV/A print """ In-plane minimization post-run: energy = ${s_pe} eV """ In-plane minimization post-run: energy = -2828.3564662776 eV if "${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 = 0.00308607949485962A < 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 = -2828.57925588218 eV ----- END PAFI ---- Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:01