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lammps/examples/USER/tally/log.12Jun17.stress.1
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log.12Jun17.stress.1
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LAMMPS (19 May 2017)
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
# make certain that shake constraints are satisfied
run 0 post no
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.358 0 -16692.358 -1289.8319
Loop time of 2e-06 on 1 procs for 0 steps with 4500 atoms
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 ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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:79)
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
Step c_press v_spa v_press v_one v_ref
0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7
10 23665.129 23665.129 23665.129 -2096059 -2096059
20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1
30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3
40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7
50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5
Loop time of 14.2089 on 1 procs for 50 steps with 4500 atoms
Performance: 0.608 ns/day, 39.469 hours/ns, 3.519 timesteps/s
32.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.983 | 12.983 | 12.983 | 0.0 | 91.37
Bond | 0.002788 | 0.002788 | 0.002788 | 0.0 | 0.02
Kspace | 0.62745 | 0.62745 | 0.62745 | 0.0 | 4.42
Neigh | 0.49839 | 0.49839 | 0.49839 | 0.0 | 3.51
Comm | 0.018597 | 0.018597 | 0.018597 | 0.0 | 0.13
Output | 0.015852 | 0.015852 | 0.015852 | 0.0 | 0.11
Modify | 0.058415 | 0.058415 | 0.058415 | 0.0 | 0.41
Other | | 0.004126 | | | 0.03
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: 0:00:15
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