From ae3a7d89016bf07a790050bb4f59d177075186b2 Mon Sep 17 00:00:00 2001 From: tomswinburne Date: Tue, 1 Sep 2020 17:02:24 +0200 Subject: [PATCH] minor changes to example --- examples/USER/misc/pafi/README | 7 + examples/USER/misc/pafi/in.pafi | 40 +-- .../USER/misc/pafi/log.15Apr20.pafi.g++.1 | 291 +++++++++++------- .../USER/misc/pafi/log.15Apr20.pafi.g++.4 | 277 ++++++++++------- 4 files changed, 370 insertions(+), 245 deletions(-) diff --git a/examples/USER/misc/pafi/README b/examples/USER/misc/pafi/README index 525dcc1e9a..c35dff313c 100644 --- a/examples/USER/misc/pafi/README +++ b/examples/USER/misc/pafi/README @@ -30,4 +30,11 @@ To run the example from this folder: mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi ``` +This example executes a hyperplane constrained overdamped Langevin simulation +whilst recording the projected free energy gradient, then minimizes in-plane, +then removes the hyperplane constraint and minimizes the whole system. +If the temperature is too high the system will leave the local minima of +the constrained system; PAFI checks for this also. + + To generate your own path, please see the LAMMPS documentation for more details diff --git a/examples/USER/misc/pafi/in.pafi b/examples/USER/misc/pafi/in.pafi index 3fcb66d0a0..9e9efb156b 100644 --- a/examples/USER/misc/pafi/in.pafi +++ b/examples/USER/misc/pafi/in.pafi @@ -48,35 +48,39 @@ variable apf equal f_af[1] run 1000 minimize 0 0 1000 1000 + +variable s_pe equal ${pe} +variable s_apf equal ${apf} +variable s_adn equal ${adn} +variable s_maxjump equal ${maxjump} + +unfix hp +unfix pa +unfix af +minimize 0 0 1000 1000 + + print """ ---------- PAFI RESULTS -------- During run: - Average Distance From Hyperplane = ${adn} A, - Average Force Projection Along MFEP = ${apf} eV/A + Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A), + Average Force Projection Along MFEP = ${s_apf} eV/A """ print """ In-plane minimization post-run: -energy = ${pe} eV +energy = ${s_pe} eV """ -if "${maxjump} > 0.1" then & -"print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" & +if "${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 = ${maxjump}A < 0.1A => No in-plane jumps'" +"print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'" print """ + +Full minimization after removal of PAFI fixes: +energy = ${pe} eV + ----- END PAFI ---- """ - - - -# disable fix and minimize full system -# unfix hp -# unfix pa -# unfix af -# minimize 0 0 1000 1000 -# print """ -# Full minimization post-run: -# energy = ${pe} eV -# """ diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 b/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 index 6413ca063a..513cbed512 100644 --- a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 +++ b/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 @@ -1,6 +1,4 @@ -LAMMPS (15 Apr 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) - using 1 OpenMP thread(s) per MPI task +LAMMPS (24 Aug 2020) units metal atom_style atomic atom_modify map array sort 0 0.0 @@ -9,16 +7,17 @@ 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 - orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872) +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 = 0.00261545 secs + read_data CPU = 0.007 seconds ## EAM potential pair_style eam/fs -pair_coeff * * Fe_mm.eam.fs Fe -Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11 +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 @@ -43,9 +42,9 @@ Neighbor list info ... 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 7.15256e-07 on 1 procs for 0 steps with 687 atoms +Loop time of 6.88e-07 on 1 procs for 0 steps with 687 atoms -139.8% CPU use with 1 MPI tasks x 1 OpenMP threads +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 @@ -55,17 +54,17 @@ 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 | | 7.153e-07 | | |100.00 +Other | | 6.88e-07 | | |100.00 -Nlocal: 687 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3239 ave 3239 max 3239 min +Nghost: 3239.00 ave 3239 max 3239 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46843 ave 46843 max 46843 min +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 = 68.1849 +Ave neighs/atom = 68.184862 Neighbor list builds = 0 Dangerous builds = 0 print "energy=${pe}" @@ -77,9 +76,9 @@ 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 4.76837e-07 on 1 procs for 0 steps with 687 atoms +Loop time of 9.41e-07 on 1 procs for 0 steps with 687 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +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 @@ -89,31 +88,31 @@ 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 | | 4.768e-07 | | |100.00 +Other | | 9.41e-07 | | |100.00 -Nlocal: 687 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3239 ave 3239 max 3239 min +Nghost: 3239.00 ave 3239 max 3239 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46843 ave 46843 max 46843 min +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 = 68.1849 +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 0 com 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 4.76837e-07 on 1 procs for 0 steps with 687 atoms +Loop time of 5.53002e-07 on 1 procs for 0 steps with 687 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +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 @@ -123,21 +122,21 @@ 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 | | 4.768e-07 | | |100.00 +Other | | 5.53e-07 | | |100.00 -Nlocal: 687 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3239 ave 3239 max 3239 min +Nghost: 3239.00 ave 3239 max 3239 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46843 ave 46843 max 46843 min +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 = 68.1849 +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 (src/min.cpp:190) +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 @@ -145,47 +144,47 @@ 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 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883 - 300 5.4507203e-14 -2828.3565 0 -2828.3565 3092.8883 - 400 5.0283346e-14 -2828.3565 0 -2828.3565 3092.8883 - 500 4.9056961e-14 -2828.3565 0 -2828.3565 3092.8883 - 600 4.8645522e-14 -2828.3565 0 -2828.3565 3092.8883 - 700 4.8498897e-14 -2828.3565 0 -2828.3565 3092.8882 - 800 4.8444578e-14 -2828.3565 0 -2828.3565 3092.8882 - 900 4.8424662e-14 -2828.3565 0 -2828.3565 3092.8882 - 1000 4.8416874e-14 -2828.3565 0 -2828.3565 3092.8882 -Loop time of 1.07709 on 1 procs for 1000 steps with 687 atoms + 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 -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -2828.24917967 -2828.35645844 -2828.35645844 - Force two-norm initial, final = 1.2831 7.46892e-07 - Force max component initial, final = 0.333171 2.93217e-07 - Final line search alpha, max atom move = 0 0 + -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 | 1.0319 | 1.0319 | 1.0319 | 0.0 | 95.80 +Pair | 1.1849 | 1.1849 | 1.1849 | 0.0 | 96.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0099187 | 0.0099187 | 0.0099187 | 0.0 | 0.92 -Output | 0.00012374 | 0.00012374 | 0.00012374 | 0.0 | 0.01 -Modify | 0.023141 | 0.023141 | 0.023141 | 0.0 | 2.15 -Other | | 0.01203 | | | 1.12 +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 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3239 ave 3239 max 3239 min +Nghost: 3239.00 ave 3239 max 3239 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46843 ave 46843 max 46843 min +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 = 68.1849 +Ave neighs/atom = 68.184862 Neighbor list builds = 0 Dangerous builds = 0 compute dx all displace/atom @@ -207,7 +206,7 @@ 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 4.8416874e-14 0 + 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 @@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump 1800 -2781.6555 512.32986 0.58277945 1900 -2782.1648 486.16736 0.58913114 2000 -2781.1942 493.15046 0.56962281 -Loop time of 1.12102 on 1 procs for 1000 steps with 687 atoms +Loop time of 1.3463 on 1 procs for 1000 steps with 687 atoms -Performance: 77.072 ns/day, 0.311 hours/ns, 892.043 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +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 | 1.0281 | 1.0281 | 1.0281 | 0.0 | 91.71 +Pair | 1.2429 | 1.2429 | 1.2429 | 0.0 | 92.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0097873 | 0.0097873 | 0.0097873 | 0.0 | 0.87 -Output | 0.00018072 | 0.00018072 | 0.00018072 | 0.0 | 0.02 -Modify | 0.080336 | 0.080336 | 0.080336 | 0.0 | 7.17 -Other | | 0.002599 | | | 0.23 +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 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3239 ave 3239 max 3239 min +Nghost: 3239.00 ave 3239 max 3239 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46844 ave 46844 max 46844 min +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 = 68.1863 +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 (src/min.cpp:190) +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 @@ -254,91 +253,149 @@ 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 5.7159207e-14 0.0017926087 - 2400 -2828.3565 5.0928432e-14 0.0020264648 + 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 4.8706709e-14 0.0024243813 - 2700 -2828.3565 4.8513394e-14 0.0026003645 - 2800 -2828.3565 4.8442921e-14 0.0027651416 - 2900 -2828.3565 4.8417392e-14 0.0029206277 - 3000 -2828.3565 4.8407328e-14 0.0030682417 -Loop time of 1.10285 on 1 procs for 1000 steps with 687 atoms + 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 -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -2781.19422469 -2828.35646618 -2828.35646619 - Force two-norm initial, final = 29.0662 7.46923e-07 - Force max component initial, final = 2.29107 2.93233e-07 - Final line search alpha, max atom move = 0 0 + -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 | 1.0574 | 1.0574 | 1.0574 | 0.0 | 95.88 +Pair | 1.2027 | 1.2027 | 1.2027 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0099056 | 0.0099056 | 0.0099056 | 0.0 | 0.90 -Output | 0.00018358 | 0.00018358 | 0.00018358 | 0.0 | 0.02 -Modify | 0.023358 | 0.023358 | 0.023358 | 0.0 | 2.12 -Other | | 0.012 | | | 1.09 +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 ave 687 max 687 min +Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3209 ave 3209 max 3209 min +Nghost: 3209.00 ave 3209 max 3209 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 48576 ave 48576 max 48576 min +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 = 70.7074 +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 = ${adn} A, - Average Force Projection Along MFEP = ${apf} eV/A + 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 = 1.36645874707752e-05 A, - Average Force Projection Along MFEP = -0.117797263023877 eV/A + 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 = ${pe} eV -""" - -In-plane minimization post-run: -energy = -2828.35646618732 eV - -if "${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'" -print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps' -Max Atomic Displacement = 0.00306824174700518A < 0.1A => No in-plane jumps -print """ ----- END PAFI ---- """ +Full minimization after removal of PAFI fixes: +energy = -2828.57925588226 eV ----- END PAFI ---- - - -#unfix hp -#unfix pa -#unfix af - -#minimize 0 0 1000 1000 -#print """ -#Full minimization post-run: -#energy = ${pe} eV -#""" - - Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:03 +Total wall time: 0:00:05 diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 b/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 index 0aa27c2956..8cda2f91c3 100644 --- a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 +++ b/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 @@ -1,6 +1,4 @@ -LAMMPS (15 Apr 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) - using 1 OpenMP thread(s) per MPI task +LAMMPS (24 Aug 2020) units metal atom_style atomic atom_modify map array sort 0 0.0 @@ -9,16 +7,17 @@ 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 - orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872) +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 = 0.00148988 secs + read_data CPU = 0.007 seconds ## EAM potential pair_style eam/fs -pair_coeff * * Fe_mm.eam.fs Fe -Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11 +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 @@ -43,9 +42,9 @@ Neighbor list info ... 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 9.17912e-06 on 4 procs for 0 steps with 687 atoms +Loop time of 2.82e-06 on 4 procs for 0 steps with 687 atoms -59.9% CPU use with 4 MPI tasks x 1 OpenMP threads +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 @@ -55,17 +54,17 @@ 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 | | 9.179e-06 | | |100.00 +Other | | 2.82e-06 | | |100.00 -Nlocal: 171.75 ave 187 max 163 min +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 +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 +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 = 68.1849 +Ave neighs/atom = 68.184862 Neighbor list builds = 0 Dangerous builds = 0 print "energy=${pe}" @@ -77,9 +76,9 @@ 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 9.11951e-06 on 4 procs for 0 steps with 687 atoms +Loop time of 2.667e-06 on 4 procs for 0 steps with 687 atoms -52.1% CPU use with 4 MPI tasks x 1 OpenMP threads +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 @@ -89,31 +88,31 @@ 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 | | 9.12e-06 | | |100.00 +Other | | 2.667e-06 | | |100.00 -Nlocal: 171.75 ave 187 max 163 min +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 +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 +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 = 68.1849 +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 0 com 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 9.17912e-06 on 4 procs for 0 steps with 687 atoms +Loop time of 2.52725e-06 on 4 procs for 0 steps with 687 atoms -84.4% CPU use with 4 MPI tasks x 1 OpenMP threads +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 @@ -123,21 +122,21 @@ 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 | | 9.179e-06 | | |100.00 +Other | | 2.527e-06 | | |100.00 -Nlocal: 171.75 ave 187 max 163 min +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 +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 +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 = 68.1849 +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 (src/min.cpp:190) +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 @@ -145,47 +144,47 @@ 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 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883 + 200 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883 300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883 - 400 5.028334e-14 -2828.3565 0 -2828.3565 3092.8883 - 500 4.905696e-14 -2828.3565 0 -2828.3565 3092.8883 - 600 4.8645524e-14 -2828.3565 0 -2828.3565 3092.8883 - 700 4.8498896e-14 -2828.3565 0 -2828.3565 3092.8882 - 800 4.8444558e-14 -2828.3565 0 -2828.3565 3092.8882 - 900 4.8424652e-14 -2828.3565 0 -2828.3565 3092.8882 - 1000 4.8416883e-14 -2828.3565 0 -2828.3565 3092.8882 -Loop time of 0.378521 on 4 procs for 1000 steps with 687 atoms + 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 -94.6% CPU use with 4 MPI tasks x 1 OpenMP threads +95.4% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -2828.24917967 -2828.35645844 -2828.35645844 - Force two-norm initial, final = 1.2831 7.46892e-07 - Force max component initial, final = 0.333171 2.93218e-07 - Final line search alpha, max atom move = 0 0 + -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 | 0.28507 | 0.30427 | 0.3132 | 2.1 | 80.38 +Pair | 0.3303 | 0.34246 | 0.35813 | 1.7 | 79.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.041108 | 0.050675 | 0.070478 | 5.2 | 13.39 -Output | 0.00013185 | 0.00025684 | 0.00063133 | 0.0 | 0.07 -Modify | 0.012176 | 0.01298 | 0.013903 | 0.7 | 3.43 -Other | | 0.01034 | | | 2.73 +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: 171.75 ave 187 max 163 min +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 +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 +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 = 68.1849 +Ave neighs/atom = 68.184862 Neighbor list builds = 0 Dangerous builds = 0 compute dx all displace/atom @@ -207,7 +206,7 @@ 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 4.8416883e-14 0 + 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 @@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump 1800 -2780.4909 519.01911 0.60204913 1900 -2782.0825 512.3441 0.6071772 2000 -2779.5449 526.21838 0.58247597 -Loop time of 0.358743 on 4 procs for 1000 steps with 687 atoms +Loop time of 0.446418 on 4 procs for 1000 steps with 687 atoms -Performance: 240.841 ns/day, 0.100 hours/ns, 2787.512 timesteps/s -97.5% CPU use with 4 MPI tasks x 1 OpenMP threads +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 | 0.2806 | 0.29275 | 0.30044 | 1.4 | 81.60 +Pair | 0.34383 | 0.35018 | 0.35655 | 0.9 | 78.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.028289 | 0.035765 | 0.047713 | 4.0 | 9.97 -Output | 0.00016427 | 0.00046188 | 0.001353 | 0.0 | 0.13 -Modify | 0.02722 | 0.027855 | 0.02832 | 0.2 | 7.76 -Other | | 0.001914 | | | 0.53 +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: 171.75 ave 183 max 165 min +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 +Nghost: 1854.25 ave 1861 max 1843 min Histogram: 1 0 0 0 0 0 1 0 1 1 -Neighs: 11711 ave 12115 max 10983 min +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 = 68.1863 +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 (src/min.cpp:190) +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 @@ -254,91 +253,149 @@ 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 5.8980022e-14 0.0018217607 - 2400 -2828.3565 5.1597338e-14 0.0020531463 - 2500 -2828.3565 4.9451625e-14 0.0022588465 + 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 4.8538712e-14 0.0026213819 - 2800 -2828.3565 4.8450182e-14 0.0027849194 - 2900 -2828.3565 4.8421015e-14 0.0029393609 - 3000 -2828.3565 4.8409029e-14 0.0030860795 -Loop time of 0.358516 on 4 procs for 1000 steps with 687 atoms + 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 -97.2% CPU use with 4 MPI tasks x 1 OpenMP threads +91.9% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -2779.54493573 -2828.35646627 -2828.35646628 - Force two-norm initial, final = 29.3013 7.46923e-07 - Force max component initial, final = 2.07903 2.93237e-07 - Final line search alpha, max atom move = 0 0 + -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 | 0.28555 | 0.30143 | 0.30793 | 1.7 | 84.08 +Pair | 0.33828 | 0.34752 | 0.35566 | 1.1 | 80.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.029324 | 0.035806 | 0.051662 | 4.9 | 9.99 -Output | 0.00016069 | 0.00043958 | 0.0012667 | 0.0 | 0.12 -Modify | 0.0087969 | 0.0089234 | 0.0090258 | 0.1 | 2.49 -Other | | 0.01192 | | | 3.32 +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: 171.75 ave 184 max 165 min +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 +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 +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 = 70.786 +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 = ${adn} A, - Average Force Projection Along MFEP = ${apf} eV/A + 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 = 1.3664587498043e-05 A, - Average Force Projection Along MFEP = -0.442220695378227 eV/A + 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 = ${pe} eV +energy = ${s_pe} eV """ In-plane minimization post-run: energy = -2828.3564662776 eV -if "${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'" -print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps' -Max Atomic Displacement = 0.00308607949101158A < 0.1A => No in-plane jumps +if "${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 ---- - - -#unfix hp -#unfix pa -#unfix af - -#minimize 0 0 1000 1000 -#print """ -#Full minimization post-run: -#energy = ${pe} eV -#""" - - Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:01