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lammps/examples/USER/tally/log.21Aug15.stress.1
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LAMMPS (21 Aug 2015-ICMS)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
group one molecule 1 2
6 atoms in group one
# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords
# compute per atom stress contributions
compute spa all stress/atom NULL pair
compute press all pressure NULL pair
# compute stress contributions from one group with all
compute c1 one stress/tally all
# collect stress contributions from all with all
compute c2 all stress/tally all
compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
#
variable spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
variable press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
variable one equal (c_one[1]+c_one[2]+c_one[3])/3.0
variable ref equal (c_one[4]+c_one[5]+c_one[6])/3.0
#velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style custom step c_press v_spa v_press v_one v_ref
thermo 10
run 50
PPPM initialization ...
G vector (1/distance) = 0.218482
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0319435
estimated relative force accuracy = 9.61968e-05
using double precision FFTs
3d grid and FFT values/proc = 8000 3375
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 6 6 6
Memory usage per processor = 24.631 Mbytes
Step press spa press one ref
0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
20 23338.149 23338.149 23338.149 -2034283 -2034283
30 25946.4 25946.4 25946.4 -2002817 -2002817
40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69
Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04
Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38
Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68
Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24
Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20
Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72
Other | | 0.002368 | | | 0.06
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21226 ave 21226 max 21226 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60175e+06 ave 2.60175e+06 max 2.60175e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601750
Ave neighs/atom = 578.167
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:04
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