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lammps/examples/python/log.5Oct16.python.g++.1
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LAMMPS (5 Oct 2016)
# 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
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 ...
1 neighbor list requests
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
Memory usage per processor = 2.69271 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 0.0323398 on 1 procs for 10 steps with 4000 atoms
Performance: 133581.484 tau/day, 309.216 timesteps/s
102.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024638 | 0.024638 | 0.024638 | 0.0 | 76.18
Neigh | 0.0063899 | 0.0063899 | 0.0063899 | 0.0 | 19.76
Comm | 0.00049949 | 0.00049949 | 0.00049949 | 0.0 | 1.54
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.06
Modify | 0.00050044 | 0.00050044 | 0.00050044 | 0.0 | 1.55
Other | | 0.0002944 | | | 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 """
def simple():
import exceptions
print "Inside simple function"
try:
foo += 1
except Exception, 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.78761 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 0.0046258 on 1 procs for 10 steps with 4000 atoms
Performance: 933893.067 tau/day, 2161.790 timesteps/s
86.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001574 | 0.001574 | 0.001574 | 0.0 | 34.03
Neigh | 0.0020421 | 0.0020421 | 0.0020421 | 0.0 | 44.14
Comm | 0.00025463 | 0.00025463 | 0.00025463 | 0.0 | 5.50
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.39
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 10.73
Other | | 0.000241 | | | 5.21
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.78761 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 0.00619817 on 1 procs for 10 steps with 4000 atoms
Performance: 696980.162 tau/day, 1613.380 timesteps/s
96.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0029786 | 0.0029786 | 0.0029786 | 0.0 | 48.06
Neigh | 0.002203 | 0.002203 | 0.002203 | 0.0 | 35.54
Comm | 0.00025678 | 0.00025678 | 0.00025678 | 0.0 | 4.14
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.29
Modify | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 7.98
Other | | 0.0002472 | | | 3.99
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.78761 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 0.00750899 on 1 procs for 10 steps with 4000 atoms
Performance: 575310.153 tau/day, 1331.736 timesteps/s
93.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.004189 | 0.004189 | 0.004189 | 0.0 | 55.79
Neigh | 0.0022991 | 0.0022991 | 0.0022991 | 0.0 | 30.62
Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 3.45
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.24
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 6.61
Other | | 0.0002475 | | | 3.30
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.78761 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 0.00869107 on 1 procs for 10 steps with 4000 atoms
Performance: 497061.786 tau/day, 1150.606 timesteps/s
103.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0049038 | 0.0049038 | 0.0049038 | 0.0 | 56.42
Neigh | 0.0027289 | 0.0027289 | 0.0027289 | 0.0 | 31.40
Comm | 0.00028753 | 0.00028753 | 0.00028753 | 0.0 | 3.31
Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.23
Modify | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 5.73
Other | | 0.0002532 | | | 2.91
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.78761 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 0.00934482 on 1 procs for 10 steps with 4000 atoms
Performance: 462288.386 tau/day, 1070.112 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0055761 | 0.0055761 | 0.0055761 | 0.0 | 59.67
Neigh | 0.002676 | 0.002676 | 0.002676 | 0.0 | 28.64
Comm | 0.00032163 | 0.00032163 | 0.00032163 | 0.0 | 3.44
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.19
Modify | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 5.34
Other | | 0.0002542 | | | 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.78761 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 0.0103869 on 1 procs for 10 steps with 4000 atoms
Performance: 415906.746 tau/day, 962.747 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0063703 | 0.0063703 | 0.0063703 | 0.0 | 61.33
Neigh | 0.002893 | 0.002893 | 0.002893 | 0.0 | 27.85
Comm | 0.00034499 | 0.00034499 | 0.00034499 | 0.0 | 3.32
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.17
Modify | 0.00050139 | 0.00050139 | 0.00050139 | 0.0 | 4.83
Other | | 0.0002594 | | | 2.50
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.78761 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 0.0116282 on 1 procs for 10 steps with 4000 atoms
Performance: 371512.205 tau/day, 859.982 timesteps/s
103.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0074186 | 0.0074186 | 0.0074186 | 0.0 | 63.80
Neigh | 0.0030658 | 0.0030658 | 0.0030658 | 0.0 | 26.37
Comm | 0.00036025 | 0.00036025 | 0.00036025 | 0.0 | 3.10
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.15
Modify | 0.0005033 | 0.0005033 | 0.0005033 | 0.0 | 4.33
Other | | 0.000263 | | | 2.26
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
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