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From: |
habib rahbari <habib.rahbari@...444...> |

Date: |
Fri, 18 Aug 2017 16:59:42 +0900 |

I would like to update my latest email.

I re-installed my lammps.

Now problem with over-boundary contacts persists, I can not get the distance which is calculated by lammps

Example : P1 position (-280.372, -299.835, 0.0), P2 position ( (-97.0773, 299.141, 0.0) Box length = 600

calculated distance by myself : 183.297560333 distance by lammps: 1.39993

Contacts that are inside bulk they have only a rounding difference

for example: P1 at (246.817, -272.008, 0.0), P2 at (247.666, -273.121, 0.0)

calculated distance is 1.39984642015 lammps distance is 1.39996

calculated distance is 1.39984642015 lammps distance is 1.39996

So contacts over boundary are doing something else!

On Fri, Aug 18, 2017 at 11:58 AM, habib rahbari <habib.rahbari@...36.....444...> wrote:

Dear Lammps developers,## for over-boundary contacts ##

I am simulating a 2D system of particles with granular hooke contact force:

pair_style gran/hooke ${knAbs} 0 ${gammanAbs} 0 0 0

pair_coeff * *

fix integr all nve/sphere

fix stick_id all enforce2d

To apply shearing, I deform the box with a shear rate shearRate:

fix boxDeform all deform 1 xy erate ${shearRate} remap v

Then I dump particles that have overlap:

compute 1 all property/local patom1 patom2 cutoff radius

and I dump distance and force between them:

compute 2 all pair/local dist force fx fy fz cutoff radius

I also dump position of all particles

dump dmp3 all custom ${dumpSteps} dump.all.* id radius mass x y z vx vy vz omegax omegay omegaz

After all, I get positions of contacting particles from the dump

files (x1, y1) and (x2, y2), then I calculate the distance between them. I consider

periodic distance between them if they have an over-boundary

contacts (this is simply done by adding/subtracting the box

length):

dx = x1 - x2

dy = y1 - y2

dx = periodic(dx)

dy = periodic(dy)

and the calculate the distance

dist = sqrt( dx * dx + dy * dy )

Then I compare this distance with the one which is provided by

Lammps in the dump file.

I am surprised that they are very different!

The difference starts from 10% up to 100%. The latter for

contacts that are over boundaries.

I have cross-checked my calculations more than a week!

Apparently for the deformed box the distance is calculated via a

different formula, maybe something like

dx = x1 - x2 -/+ shearRate * (some time scale) * (box length)

Would you mind please let me know how the distance in deformed

box is calculated.

Can you refer me to to that line in the code so I can see it exactly.

In advance, I appreciate your kind help.

--

--

**References**:**[lammps-users] Distance between particles does not match for deformed box***From:*habib rahbari <habib.rahbari@...444...>

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