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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.

Steve

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...>Hi!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 willdivide extensive quantities by N (by default) See the docpage for the units and thermo_style and thermo_modify commands.SteveOn Mon, Nov 20, 2017 at 9:21 PM, yu han <wildheart6143@...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 feneread_data 30.softall

neighbor 0.4 bin

neigh_modify every 1 delay 1bond_style fene

bond_coeff 1 30.0 1.5 1.0 1.0pair_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 lofix ff0 gvv setforce 0 0 0

fix 09 hi addforce 0 0 -10.0

fix 22 lo setforce 0.0 0.0 0variable 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 10000thermo 100

timestep 0.005

dump 1 all custom 100 ./dumpaddforce/dump*.coordinate id type x y z fz

run 100000------------------------------ ------------------

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**References**:**[lammps-users] compute group/group in a different model***From:*yu han <wildheart6143@...24...>

**Re: [lammps-users] compute group/group in a different model***From:*Steve Plimpton <sjplimp@...24...>

**[lammps-users] Fwd: compute group/group in a different model***From:*yu han <wildheart6143@...24...>

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