Two basic queries

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1

  1. In a region if i want to delete some specific atoms whose group id is known to me, So how can I do through delete_atoms command in lammps ( need to specify both the region and group id for that particular atom)?

  2. compute myPress water temp/region inner
    thermo_modify Press myPress

For pressure calculation the error message is that:
ERROR: Thermo_modify pressure ID does not compute pressure (…/thermo.cpp:480)

Why this command is not working for the calculation of pressure can anyone give me any suggestion?

2

Tuhin Samanta
Prof. Biman Bagchi’s lab

SSCU

IISC

Bangalore- 560012

3

1. In a region if i want to delete some specific atoms whose group id is
known to me, So how can I do through delete_atoms command in lammps ( need
to specify both the region and group id for that particular atom)?

No, just the group id is fine.

2. compute myPress water temp/region inner

Because this is compute temp/region...

Ray

4

First of all thanks for your suggestion…But

  1. Actually with in a simulation box i have chosen a block, now i want to calculate the pressure with in that block where atoms are free to move in/out of that block region. So i think this temp/region should be used to calculate the pressure for that region … what is your opinion about that or any other command?

  2. And for another part when i am choosing a region its considering two types of particles with in that region but i want to calculate the pressure of that region for one kinds of particle . How can i do that if you can suggest me anything please suggest…

5

Tuhin Samanta
Prof. Biman Bagchi's lab
SSCU
IISC
Bangalore- 560012

From: Tuhin Samanta <[email protected]...>
Date: Wed, Feb 25, 2015 at 10:43 PM
Subject: Two basic queries
To: LAMMPS <[email protected]>

1. In a region if i want to delete some specific atoms whose group id is
known to me, So how can I do through delete_atoms command in lammps ( need
to specify both the region and group id for that particular atom)?

2.

compute myPress water temp/region inner
compute_modify myPress dynamic yes extra 600
thermo_modify Press myPress

For pressure calculation the error message is that:
ERROR: Thermo_modify pressure ID does not compute pressure
(../thermo.cpp:480)

You definitely cannot calculate pressure with a compute that calculates
temperature...

Can you suggest me anything..

http://lammps.sandia.gov/doc/compute_stress_atom.html

Ray

6

First of all thanks for your suggestion.............But

1. Actually with in a simulation box i have chosen a block, now i want to
calculate the pressure with in that block where atoms are free to move
in/out of that block region. So i think this temp/region should be used to
calculate the pressure for that region .... what is your opinion about
that or any other command?

compute temp/region, by the name TEMP, calculates temperature ...
Temperature is not Pressure.

2. And for another part when i am choosing a region its considering two
types of particles with in that region but i want to calculate the pressure
of that region for one kinds of particle . How can i do that if you can
suggest me anything please suggest.................

This does not make sense at all.

Ray

7

Okk i will try to calculate with stress per atom but for this one

And for another part when i am choosing a region its considering two types of particles with in that region but i want to calculate the pressure of that region for one kinds of particle . How can i do that if you can suggest me anything please suggest…

8

Actually when i am choosing a region its considering two types of particles with in that region ( my system consist of two kinds of particles) but i want to calculate the pressure of that region for one types of particle . Is there any way ?

9

Actually when i am choosing a region its considering two types of
particles with in that region ( my system consist of two kinds of
particles) but i want to calculate the pressure of that region for one
types of particle . Is there any way ?

​can you show us a derivation for how this needs to be computed?​

​to infer pressure from virial stress, you need a volume and that is an ill
defined property under your conditions.

axel.​

10

Yes, you are right to calculate the pressure from virial stress we need
volume. Actually i have prepared two wall with in a simulation box and i am
trying to calculate the pressure with in that region but as i have chosen a
region somehow wall particles are also taken into account but i want to
remove the wall particles to calculate the pressure .............