From 77f009126a057b268e50cf00e5520f5bc84cfcb1 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 2 Jun 2021 12:12:17 -0600 Subject: [PATCH] Fixing comments and log files --- examples/tracker/log.8Apr21.melt.g++.1 | 0 examples/tracker/log.8Apr21.tracker.g++.1 | 107 ++++++++++++++++++++++ src/MISC/fix_pair_tracker.cpp | 5 +- 3 files changed, 109 insertions(+), 3 deletions(-) delete mode 100644 examples/tracker/log.8Apr21.melt.g++.1 create mode 100644 examples/tracker/log.8Apr21.tracker.g++.1 diff --git a/examples/tracker/log.8Apr21.melt.g++.1 b/examples/tracker/log.8Apr21.melt.g++.1 deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/examples/tracker/log.8Apr21.tracker.g++.1 b/examples/tracker/log.8Apr21.tracker.g++.1 new file mode 100644 index 0000000000..e654558061 --- /dev/null +++ b/examples/tracker/log.8Apr21.tracker.g++.1 @@ -0,0 +1,107 @@ +LAMMPS (8 Apr 2021) +# 3d Lennard-Jones melt with tracking + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 256 atoms + create_atoms CPU = 0.001 seconds +mass 1 1.0 +mass 2 1.0 +velocity all create 2.0 87287 loop geom + +pair_style hybrid/overlay lj/cut 2.5 tracker +pair_coeff * * lj/cut 1.0 1.0 2.5 +pair_coeff * * tracker 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve +fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5 +fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat + +dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4] +dump_modify 1 header no + +# compute 1 all property/local patom1 patom2 +# dump 2 all local 1 pairs.dat c_1[1] c_1[2] + +# dump 3 all atom 1 atoms.dat + +thermo 50 +run 1000 #0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) pair tracker, perpetual + attributes: half, newton on, history + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 2 -6.7733681 0 -3.7850868 -4.5535126 + 50 1.0540428 -5.3670859 0 -3.7921977 2.3386375 + 100 1.0402713 -5.3493439 0 -3.7950323 2.4553748 + 150 1.0570745 -5.3738961 0 -3.7944781 2.3767396 + 200 1.0431846 -5.3518647 0 -3.7932002 2.5010135 + 250 1.070121 -5.3902744 0 -3.791363 2.4908658 + 300 1.0667723 -5.3866302 0 -3.7927224 2.3589344 + 350 1.000601 -5.2859643 0 -3.7909257 2.9065274 + 400 0.99256113 -5.2738812 0 -3.7908553 2.8595867 + 450 1.0482542 -5.357452 0 -3.7912128 2.4707397 + 500 1.0196176 -5.3123538 0 -3.7889017 2.7230338 + 550 0.98274535 -5.2586303 0 -3.7902706 2.9156947 + 600 1.0683914 -5.3863229 0 -3.789996 2.3002719 + 650 1.0130779 -5.303917 0 -3.7902362 2.8726423 + 700 1.0583333 -5.3737358 0 -3.792437 2.5770307 + 750 0.98274506 -5.2612464 0 -3.792887 2.9447027 + 800 1.0294191 -5.332001 0 -3.7939042 2.5293193 + 850 0.99240027 -5.2735754 0 -3.7907899 2.7672711 + 900 1.0293488 -5.3306241 0 -3.7926323 2.6054041 + 950 0.97137182 -5.2424403 0 -3.7910742 3.129989 + 1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598 +Loop time of 0.310363 on 1 procs for 1000 steps with 256 atoms + +Performance: 1391918.252 tau/day, 3222.033 timesteps/s +100.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.22132 | 0.22132 | 0.22132 | 0.0 | 71.31 +Neigh | 0.03458 | 0.03458 | 0.03458 | 0.0 | 11.14 +Comm | 0.0087938 | 0.0087938 | 0.0087938 | 0.0 | 2.83 +Output | 0.014075 | 0.014075 | 0.014075 | 0.0 | 4.54 +Modify | 0.02818 | 0.02818 | 0.02818 | 0.0 | 9.08 +Other | | 0.003411 | | | 1.10 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1327.00 ave 1327 max 1327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9612.00 ave 9612 max 9612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9612 +Ave neighs/atom = 37.546875 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/src/MISC/fix_pair_tracker.cpp b/src/MISC/fix_pair_tracker.cpp index 3feffa27c4..a709792216 100644 --- a/src/MISC/fix_pair_tracker.cpp +++ b/src/MISC/fix_pair_tracker.cpp @@ -256,9 +256,8 @@ double FixPairTracker::memory_usage() } /* ---------------------------------------------------------------------- - one method for every keyword fix property/local can output - the atom property is packed into buf starting at n with stride nvalues - customize a new keyword by adding a method + one method for every keyword fix pair/tracker can output + the atom property is packed into a local vector or array ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */