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.fix_python_invoke.g++.1
+++ b/examples/python/log.27Nov18.fix_python_invoke.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 = 0.000678539 secs
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+python         end_of_step_callback here """
+from __future__ import print_function
+from lammps import lammps
+def end_of_step_callback(lmp):
+  L = lammps(ptr=lmp)
+  t = L.extract_global("ntimestep", 0)
+  print("### END OF STEP ###", t)
+def post_force_callback(lmp, v):
+  L = lammps(ptr=lmp)
+  t = L.extract_global("ntimestep", 0)
+  print("### POST_FORCE ###", t)
+"""
+
+fix		1 all nve
+fix     2 all python/invoke 50 end_of_step end_of_step_callback
+fix     3 all python/invoke 50 post_force post_force_callback
+
+#dump		id all atom 50 dump.melt
+
+#dump		2 all image 25 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+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 lj/cut, 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   -6.7733681            0   -2.2744931   -3.7033504 
+      50    1.6758903   -4.7955425            0   -2.2823355     5.670064 
+     100    1.6458363   -4.7492704            0   -2.2811332    5.8691042 
+     150    1.6324555   -4.7286791            0    -2.280608    5.9589514 
+     200    1.6630725   -4.7750988            0   -2.2811136    5.7364886 
+     250    1.6275257   -4.7224992            0    -2.281821    5.9567365 
+Loop time of 0.732007 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 147539.519 tau/day, 341.527 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.60651    | 0.60651    | 0.60651    |   0.0 | 82.86
+Neigh   | 0.092702   | 0.092702   | 0.092702   |   0.0 | 12.66
+Comm    | 0.013686   | 0.013686   | 0.013686   |   0.0 |  1.87
+Output  | 0.00016069 | 0.00016069 | 0.00016069 |   0.0 |  0.02
+Modify  | 0.016055   | 0.016055   | 0.016055   |   0.0 |  2.19
+Other   |            | 0.00289    |            |       |  0.39
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5499 ave 5499 max 5499 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    151513 ave 151513 max 151513 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 151513
+Ave neighs/atom = 37.8783
+Neighbor list builds = 12
+Dangerous builds not checked
+Total wall time: 0:00:00