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lammps/examples/USER/tally/log.12Jun17.force.4
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log.12Jun17.force.4
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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)
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
# 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 = 3380 960
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) = 10.6 | 10.61 | 10.61 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.358 0 -16692.358 -1289.8319
Loop time of 4.5e-06 on 4 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 force/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
variable all equal round(1e10*c_c2)*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 v_all
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 = 3380 960
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
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
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute group/group, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.59 | 11.6 Mbytes
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 v_all
0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0
10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0
20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0
30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0
40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0
50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0
Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms
Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s
31.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5075 | 3.6114 | 3.7489 | 4.7 | 83.67
Bond | 8.6e-05 | 0.00010525 | 0.000141 | 0.0 | 0.00
Kspace | 0.2581 | 0.39489 | 0.49723 | 14.2 | 9.15
Neigh | 0.19826 | 0.19888 | 0.19918 | 0.1 | 4.61
Comm | 0.034639 | 0.037137 | 0.038938 | 0.9 | 0.86
Output | 0.025465 | 0.025997 | 0.027558 | 0.6 | 0.60
Modify | 0.044022 | 0.044175 | 0.044407 | 0.1 | 1.02
Other | | 0.003593 | | | 0.08
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 = 2601983
Ave neighs/atom = 578.218
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1
Total wall time: 0:00:04
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