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lammps/examples/USER/tally/log.21Aug15.force.4
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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)
2 by 2 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 pe/tally compute and other computes and thermo keywords
# compute pairwise force between two molecules and everybody
compute fpa one group/group all pair yes kspace no boundary no
# tally pairwise force between two molecules and the all molecules
compute c1 one force/tally all
# tally the force of all with all (should be zero)
compute c2 all force/tally all
# collect per atom data. only reduce over the first group.
compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
# determine magnitude of force
variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
# round to 10**-10 absolute precision.
variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
velocity all create 300 432567 dist uniform
timestep 2.0
# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2
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 = 3380 960
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
Neighbor list info ...
2 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 = 8.16441 Mbytes
Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
Loop time of 1.13658 on 4 procs for 50 steps with 4500 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 7.602 ns/day 3.157 hours/ns 43.991 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38
Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00
Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25
Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56
Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59
Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21
Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86
Other | | 0.001656 | | | 0.15
Nlocal: 1125 ave 1148 max 1097 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 12212.5 ave 12269 max 12162 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 650496 ave 675112 max 631353 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 2601984
Ave neighs/atom = 578.219
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1
Total wall time: 0:00:01
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