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lammps/examples/python/log.python.17Mar15.linux.1
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LAMMPS (12 Mar 2015)
# 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
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
master list distance cutoff = 2.8
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 0.03213 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.0242701 (75.5371)
Neigh time (%) = 0.006531 (20.3268)
Comm time (%) = 0.000502825 (1.56497)
Outpt time (%) = 2.09808e-05 (0.0652998)
Other time (%) = 0.00080514 (2.50588)
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
master list distance cutoff = 1.3
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 0.00451207 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00158691 (35.1704)
Neigh time (%) = 0.00194287 (43.0594)
Comm time (%) = 0.000257015 (5.69617)
Outpt time (%) = 2.09808e-05 (0.464993)
Other time (%) = 0.000704288 (15.609)
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
master list distance cutoff = 1.4
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 0.00607896 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00298262 (49.0646)
Neigh time (%) = 0.00210714 (34.6629)
Comm time (%) = 0.000262499 (4.31816)
Outpt time (%) = 2.00272e-05 (0.329451)
Other time (%) = 0.000706673 (11.6249)
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
master list distance cutoff = 1.5
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 0.00735807 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00416398 (56.5906)
Neigh time (%) = 0.00219989 (29.8976)
Comm time (%) = 0.000262022 (3.56101)
Outpt time (%) = 1.90735e-05 (0.259218)
Other time (%) = 0.00071311 (9.69153)
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
master list distance cutoff = 1.6
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 0.0085659 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00486517 (56.7969)
Neigh time (%) = 0.00266886 (31.1568)
Comm time (%) = 0.000301838 (3.52371)
Outpt time (%) = 2.00272e-05 (0.233801)
Other time (%) = 0.000710011 (8.2888)
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
master list distance cutoff = 1.7
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 0.0091939 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00552583 (60.1032)
Neigh time (%) = 0.00259781 (28.2558)
Comm time (%) = 0.000323296 (3.51642)
Outpt time (%) = 2.00272e-05 (0.217831)
Other time (%) = 0.000726938 (7.90675)
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
master list distance cutoff = 1.8
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 0.0102301 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00630403 (61.6225)
Neigh time (%) = 0.00282717 (27.6359)
Comm time (%) = 0.000349283 (3.41428)
Outpt time (%) = 2.00272e-05 (0.195768)
Other time (%) = 0.000729561 (7.13154)
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
master list distance cutoff = 1.9
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 0.011508 on 1 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00736189 (63.972)
Neigh time (%) = 0.00303006 (26.3301)
Comm time (%) = 0.000365019 (3.17187)
Outpt time (%) = 2.00272e-05 (0.174028)
Other time (%) = 0.000730991 (6.35203)
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
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