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Re: [lammps-users] compute group/group in a different model
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Re: [lammps-users] compute group/group in a different model


From: Steve Plimpton <sjplimp@...24...>
Date: Tue, 21 Nov 2017 09:05:41 -0700

If you are using LJ units then the thermo output will
divide extensive quantities by N (by default)  See the doc
page for the units and thermo_style and thermo_modify commands.

Steve

On Mon, Nov 20, 2017 at 9:21 PM, yu han <wildheart6143@...36.....24...> wrote:

Hi!
It’s my first time to write my question to you with this method. I don’t know if the method is right. And if there is any trouble with you, I am sorry.
My problem is about a force of two group. In simple terms, my model is that the middle layer of polymer chains is pressed with two fcc cryatal. What I need to calculate is the pressure between layer and the upper crystal. The units id LJ,and the command is compute group/group. And I found the force is equal with different size of model in a same load(the load way via the command of “addforce”). In other words, The force output by thermo_style with ADDFORCE command at the same load should increase proportionally. However ,the result is identical.
And then I read the manual of units and group/group command!
The manual say that force in three direction are “extensive”, and extensive quantities are output by SUM/ATOM. What? This is contrary to the group/group command/
In the next I tested the easy model with different size. And I got the same conclusion.
And can you tell me where I have wrong?
The following is my in.test.
units lj
atom_style bond
dimension 3
boundary p p s
special_bonds fene

read_data 30.softall

neighbor 0.4 bin
neigh_modify every 1 delay 1

bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0

pair_style hybrid lj/cut 2.0
pair_modify shift yes
pair_coeff 1 1 lj/cut 1.0 1.0 
pair_coeff 1 2 lj/cut 1.0 1.0 
pair_coeff 1 3 lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.0 1.0 
pair_coeff 3 3 lj/cut 1.0 1.0 
pair_coeff 2 3 lj/cut 1.0 1.0 
pair_coeff * 4 none

atom regions

region lo-fixed block INF INF INF INF INF -11.937
region hi-fixed block INF INF INF INF 11.937 INF
group lo region lo-fixed
group hi region hi-fixed
group boundary union lo hi
group mobile subtract all boundary
group up type 2
group chain type 1
group down type 3
group gvv type 4
group bcchi subtract up hi
group bcclo subtract down lo
group slide subtract all lo

fix ff0 gvv setforce 0 0 0
fix 09 hi addforce 0 0 -10.0
fix 22 lo setforce 0.0 0.0 0

variable temp equal 0.001
fix relax all nve
velocity mobile create ${temp} 482748 rot yes dist gaussian
fix 35 mobile temp/berendsen ${temp} ${temp} 0.2
compute friction33 chain group/group bcchi
compute friction22 chain group/group chain compute friction11 bcclo group/group chain
compute friction44 bcchi group/group hi
compute friction55 bcclo group/group lo
compute friction66 chain group/group up

compute

compute 99 chain stress/atom NULL
compute 100 chain reduce sum c_99[1] c_99[2] c_99[3]
compute 111 bcchi property/atom fz
compute 122 bcchi reduce sum c_111 
compute 113 hi property/atom fz
compute 124 hi reduce sum c_113
compute 114 bcclo property/atom fz
compute 125 bcclo reduce sum c_114
compute 222 all temp 
thermo_style custom step c_friction33[3] c_friction33[1] c_friction11[3] c_friction11[1]
minimize 1.0e-6 1.0e-8 1000 10000

thermo 100
timestep 0.005
dump 1 all custom 100 ./dumpaddforce/dump*.coordinate id type x y z fz
run 100000


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