update log files for peptide, peri, pour and python examples

2018-11-29 14:51:25 -05:00
parent cef4164460
commit 46bf4b7efb
39 changed files with 1843 additions and 1353 deletions
--- a/examples/python/log.27Nov18.pair_python_table.g++.1
+++ b/examples/python/log.27Nov18.pair_python_table.g++.1
@ -0,0 +1,100 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 10 0 10 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 4000 atoms
+  Time spent = 0.000697136 secs
+mass		* 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	python 2.5
+pair_coeff	* * py_pot.LJCutMelt lj
+
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair python, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+
+pair_style      table linear 2000
+pair_coeff      1 1 lj_1_1.table LJ
+WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (src/pair_table.cpp:481)
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+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 = 12 12 12
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, 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) = 3.221 | 3.221 | 3.221 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            3   -6.7733629            0   -2.2744879   -3.7032813 
+      50    1.6758731   -4.7953067            0   -2.2821255    5.6706553 
+     100    1.6458118   -4.7490281            0   -2.2809276    5.8697466 
+     150     1.632425   -4.7284533            0   -2.2804279    5.9595684 
+     200    1.6631578   -4.7749889            0   -2.2808759    5.7365839 
+     250    1.6277062   -4.7224727            0   -2.2815238    5.9572913 
+Loop time of 0.94897 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 113807.650 tau/day, 263.444 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.82415    | 0.82415    | 0.82415    |   0.0 | 86.85
+Neigh   | 0.093798   | 0.093798   | 0.093798   |   0.0 |  9.88
+Comm    | 0.013542   | 0.013542   | 0.013542   |   0.0 |  1.43
+Output  | 0.00017834 | 0.00017834 | 0.00017834 |   0.0 |  0.02
+Modify  | 0.014418   | 0.014418   | 0.014418   |   0.0 |  1.52
+Other   |            | 0.002882   |            |       |  0.30
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    151496 ave 151496 max 151496 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 151496
+Ave neighs/atom = 37.874
+Neighbor list builds = 12
+Dangerous builds not checked
+
+shell rm lj_1_1.table
+
+Total wall time: 0:00:00