pair/gran/local dump local file dumping lot of zeros

Submitted by prasantud on Wed, 10/26/2011 - 08:50

Hi everybody,
The output file of the following programme dumps lot of zeros even in atomic ids.
Could you give some explanation?

###### programme starts here ##########
units si

atom_style granular
atom_modify map array
boundary f p f
newton off

# Read data
read_data Ordored_Liggghts_long.sys

set group all diameter 0.10

communicate single vel yes

neighbor 0.001 bin
neigh_modify delay 0

#Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 1.e6
fix m2 all property/global poissonsRatio peratomtype 0.3
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.9
fix m4 all property/global coefficientFriction peratomtypepair 1 0.05
fix m5 all property/global characteristicVelocity scalar 2.
fix m6 all property/global cohesionEnergyDensity peratomtypepair 1 200

#New pair style
pair_style gran/hertz/history 1 1 #Hertzian with cohesion
pair_coeff * *

timestep 0.0002
variable dump_every equal 1000

fix gravi all gravity 9.81 vector 0.0 0.0 -1.0
fix xwall1 all wall/gran/hertz/history 1 0 xplane -0.05 1.05 1
fix zwall1 all wall/gran/hertz/history 1 0 zplane -0.05 1.04 1

fix integ all nve/sphere

compute str all stress/atom ke pair
compute p all reduce sum c_str[1] c_str[2] c_str[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)

compute forces all pair/gran/local pos id force
compute_modify thermo_temp dynamic yes
thermo_style custom step atoms ke vol v_press
thermo ${dump_every}
thermo_modify lost ignore norm no

run 1
dump forcedump all local 10000 post/dump.del c_forces[1] c_forces[2] c_forces[3] c_forces[4] c_forces[5] c_forces[6] c_forces[7] c_forces[8] c_forces[9] c_forces[10] c_forces[11] c_forces[12]

run 10000 upto
######## programme ends ###############

####### output on teerminal ##########3

Nlocal: 562.333 ave 564 max 560 min
Histogram: 1 0 0 0 0 0 0 1 0 1
Nghost: 286 ave 290 max 283 min
Histogram: 1 0 1 0 0 0 0 0 0 1
Neighs: 3252.33 ave 3303 max 3201 min
Histogram: 1 0 0 0 0 1 0 0 0 1

Total # of neighbors = 9757
Ave neighs/atom = 5.78364
Neighbor list builds = 2484
Dangerous builds = 0

############################

The file dump.del has data for 4120 lines.
There are zeros on all columns for total 4437 lines
1318-2799, 4137-5621 and 7093-8562.

It calculated total 9757 neighbors printed on the terminal,
But the output file is only 8562 lines of which 4437 lines are all zeros.

Regards,
Samantaray

ckloss's picture

ckloss | Wed, 10/26/2011 - 11:40

there is a small glitch in compute pair/gran/local that will be corrected in the next version
Don't know if that is the cause but it is likely

Christoph