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

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Axel Kohlmeyer
2018-11-29 14:51:25 -05:00
parent cef4164460
commit 46bf4b7efb
39 changed files with 1843 additions and 1353 deletions
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examples/python/log.27Nov18.python.g++.1 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt with Python functions added
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 = 0.00072813 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
run 10
Neighbor list info ...
update every 1 steps, delay 0 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 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) = 3.721 | 3.721 | 3.721 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.0312054 on 1 procs for 10 steps with 4000 atoms
Performance: 138437.508 tau/day, 320.457 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022328 | 0.022328 | 0.022328 | 0.0 | 71.55
Neigh | 0.0073318 | 0.0073318 | 0.0073318 | 0.0 | 23.50
Comm | 0.0006578 | 0.0006578 | 0.0006578 | 0.0 | 2.11
Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.09
Modify | 0.00057721 | 0.00057721 | 0.00057721 | 0.0 | 1.85
Other | | 0.0002832 | | | 0.91
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5841 ave 5841 max 5841 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155984 ave 155984 max 155984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155984
Ave neighs/atom = 38.996
Neighbor list builds = 1
Dangerous builds = 0
# 1st Python function
# example of catching a syntax error
python simple here """
from __future__ import print_function
def simple():
foo = 0
print("Inside simple function")
try:
foo += 1
except Exception as e:
print("FOO error:", e)
"""
python simple invoke
# 2nd Python function
# example of returning the function value to a python-style variable
# invoke it twice
variable fact python factorial
python factorial input 1 v_n return v_fact format ii here """
def factorial(n):
if n == 1: return 1
return n*factorial(n-1)
"""
variable n string 10
python factorial invoke
print "Factorial of $n = ${fact}"
Factorial of 10 = 3628800
variable n string 20
python factorial invoke
print "Factorial of $n = ${fact}"
Factorial of 20 = 2432902008176640000
# 3rd Python function
# example of calling back to LAMMPS and writing a run loop in Python
variable cut string 0.0
python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
python loop invoke
pair_style lj/cut ${cut}
pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.00488138 on 1 procs for 10 steps with 4000 atoms
Performance: 884995.276 tau/day, 2048.600 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 35.17
Neigh | 0.0020256 | 0.0020256 | 0.0020256 | 0.0 | 41.50
Comm | 0.00028539 | 0.00028539 | 0.00028539 | 0.0 | 5.85
Output | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.55
Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 11.76
Other | | 0.0002532 | | | 5.19
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2083 ave 2083 max 2083 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17727 ave 17727 max 17727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17727
Ave neighs/atom = 4.43175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00647616 on 1 procs for 10 steps with 4000 atoms
Performance: 667061.565 tau/day, 1544.124 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 | 0.0030439 | 0.0030439 | 0.0030439 | 0.0 | 47.00
Neigh | 0.002295 | 0.002295 | 0.002295 | 0.0 | 35.44
Comm | 0.00028467 | 0.00028467 | 0.00028467 | 0.0 | 4.40
Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.37
Modify | 0.0005753 | 0.0005753 | 0.0005753 | 0.0 | 8.88
Other | | 0.0002534 | | | 3.91
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2087 ave 2087 max 2087 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21036 ave 21036 max 21036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21036
Ave neighs/atom = 5.259
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00802207 on 1 procs for 10 steps with 4000 atoms
Performance: 538514.378 tau/day, 1246.561 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0044219 | 0.0044219 | 0.0044219 | 0.0 | 55.12
Neigh | 0.0024219 | 0.0024219 | 0.0024219 | 0.0 | 30.19
Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 3.75
Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.32
Modify | 0.00059366 | 0.00059366 | 0.00059366 | 0.0 | 7.40
Other | | 0.0002577 | | | 3.21
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2250 ave 2250 max 2250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24095 ave 24095 max 24095 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24095
Ave neighs/atom = 6.02375
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00908327 on 1 procs for 10 steps with 4000 atoms
Performance: 475599.593 tau/day, 1100.925 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0049157 | 0.0049157 | 0.0049157 | 0.0 | 54.12
Neigh | 0.0029771 | 0.0029771 | 0.0029771 | 0.0 | 32.78
Comm | 0.00033617 | 0.00033617 | 0.00033617 | 0.0 | 3.70
Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.25
Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 6.34
Other | | 0.0002553 | | | 2.81
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2572 ave 2572 max 2572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27137 ave 27137 max 27137 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 27137
Ave neighs/atom = 6.78425
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.0096159 on 1 procs for 10 steps with 4000 atoms
Performance: 449256.007 tau/day, 1039.944 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0054793 | 0.0054793 | 0.0054793 | 0.0 | 56.98
Neigh | 0.0028973 | 0.0028973 | 0.0028973 | 0.0 | 30.13
Comm | 0.00038075 | 0.00038075 | 0.00038075 | 0.0 | 3.96
Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.24
Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 5.97
Other | | 0.0002615 | | | 2.72
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3013 ave 3013 max 3013 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 30887 ave 30887 max 30887 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30887
Ave neighs/atom = 7.72175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.0107083 on 1 procs for 10 steps with 4000 atoms
Performance: 403424.172 tau/day, 933.852 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0062652 | 0.0062652 | 0.0062652 | 0.0 | 58.51
Neigh | 0.0031667 | 0.0031667 | 0.0031667 | 0.0 | 29.57
Comm | 0.00041771 | 0.00041771 | 0.00041771 | 0.0 | 3.90
Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.21
Modify | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 5.35
Other | | 0.0002627 | | | 2.45
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3388 ave 3388 max 3388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35959 ave 35959 max 35959 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35959
Ave neighs/atom = 8.98975
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0
run 10
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.0121632 on 1 procs for 10 steps with 4000 atoms
Performance: 355170.795 tau/day, 822.155 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0074623 | 0.0074623 | 0.0074623 | 0.0 | 61.35
Neigh | 0.0033951 | 0.0033951 | 0.0033951 | 0.0 | 27.91
Comm | 0.00043678 | 0.00043678 | 0.00043678 | 0.0 | 3.59
Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.20
Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 4.73
Other | | 0.0002692 | | | 2.21
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3612 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 43239 ave 43239 max 43239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43239
Ave neighs/atom = 10.8097
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00