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

From: Steve Plimpton <sjplimp@...24...>
Date: Wed, 22 Nov 2017 09:41:51 -0700

All the thermo output is doing for extensive vs intensive
is dividing by N = total # of atoms.  Thermo output knows
nothing about groups or the size of groups. You can undo or do
the factor of N yourself in many ways.


On Tue, Nov 21, 2017 at 10:14 PM, yu han <wildheart6143@...24...> wrote:

---------- Forwarded message ----------
From: yu han <wildheart6143@...24...>
Date: 2017-11-22 13:09 GMT+08:00
Subject: Re: [lammps-users] compute group/group in a different model
To: Steve Plimpton <sjplimp@...24...>

Thanks your reply!
The question is that  if the thermo output is divided extensive quantities by N,then how to get the extensive quantities and which atoms of group need to be multiplied? because the two groups which were computed are not similar.

2017-11-22 0:05 GMT+08:00 Steve Plimpton <sjplimp@...24...>:
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.


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

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 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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