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[lammps-users] reg_unknown number of entries in pair/local
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[lammps-users] reg_unknown number of entries in pair/local


From: santhosh mathesan <sans.aero@...24...>
Date: Tue, 22 May 2018 19:25:46 +0300

Dear all,

I am trying to obtain force acting on atom i due to atom j in a gold system during the deformation process. I did used a unit cell (simple system) to check whether pair/local calculates the forces for all the pairs within the system. I am not sure why the number of entries are more than the combination expected from the system.

units metal
atom_style atomic
boundary p p p 

lattice fcc 4.08 orient x 1 0 0  orient y 0 1 0 orient z 0 0 1 origin 0.05 0.05 0.05
region sim_region block 0 1 0 1 0 1 units lattice
create_box 1 sim_region
create_atoms 1 box

pair_style eam/alloy
pair_coeff * * Au_GLJ10_3.eam.alloy Au


dump 1 all atom 100 dump_min.atom
thermo 100
thermo_style custom step pe press vol etotal
min_style cg
minimize 1e-15 1e-7 70000 100000
print "MINIMIZATION DONE"
undump 1

write_data aftermin.txt

dump 2 all atom 1000 dump_for_deform.atom
variable tmp equal "lx"
variable L0 equal ${tmp}
variable strain equal "(lx - v_L0)/v_L0"
variable p1 equal "v_strain"
variable p2 equal "-pxx*0.0001"

variable srate equal 1.0e9
variable srate1 equal "v_srate/1.0e12"

fix 1 all nve
fix 2 all deform 1 x erate ${srate1} units box remap x
thermo_style custom step temp vol density pe ke etotal pxx pyy pzz lx ly lz 
thermo          1000
timestep 0.001

compute 1 all property/local patom1 patom2
compute 2 all pair/local dist fx fy fz
dump 1 all local 1 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3] c_2[4]

run 1
undump 2
unfix 1
unfix 2

The output from dump file is 

ITEM: TIMESTEP
1
ITEM: NUMBER OF ENTRIES
108
ITEM: BOX BOUNDS pp pp pp
0 4.08
0 4.08
0 4.08
ITEM: ENTRIES index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3] c_2[4] 
1 1 2 2.885 -0.0711631 -0.0711631 0 
2 1 3 2.885 -0.0711631 0 -0.0711631 
3 1 4 2.885 0 -0.0711631 -0.0711631 
4 1 1 4.08 0.0463516 -0 -0 
5 1 4 4.99696 0.0165693 0.00828464 0.00828464 
6 1 1 5.76999 -0.000857057 0.000857057 -0 
7 1 3 4.99696 -0.00828464 0.0165693 0.00828464 
8 1 1 4.08 -0 0.0463516 -0 
9 1 3 4.99696 0.00828464 0.0165693 0.00828464 
10 1 1 5.76999 0.000857057 0.000857057 -0 
11 1 2 4.99696 -0.00828464 -0.00828464 0.0165693 
12 1 1 5.76999 -0 -0.000857057 0.000857057 
13 1 2 4.99696 0.00828464 -0.00828464 0.0165693 
14 1 1 5.76999 -0.000857057 -0 0.000857057 
15 1 2 4.99696 -0.00828464 0.00828464 0.0165693 
16 1 1 4.08 -0 -0 0.0463516 
17 1 2 4.99696 0.00828464 0.00828464 0.0165693 
18 1 1 5.76999 0.000857057 -0 0.000857057 
19 1 1 5.76999 -0 0.000857057 0.000857057 

I would like to know why there are more than " 1 2 " atom combination in the output.

Suggestions please.

Regards, 
Santhosh