The ABINIT Users Mailing List ( CLOSED )

[Zeila Zanolli <zeila.zanolli@uclouvain.be>]

Hi,

just give the character of being "executable" to abi2xsf, that is, go in the directory where abi2xsf is located and type:

   chmod +x abi2xsf

Just google for 'chmod' to know more about this command.... for instance:

http://en.wikipedia.org/wiki/Chmod

Now you will have the permission to execute abi2xsf.

In addition, as i have already mentioned in the provious mail, the way to use this script is written in the script itself,

so you wont get the .xsf by doing:

/home/dev/abinit-5.8.4/util/users/abi2xsf <t08.out> try.xsf 

To know how to use it, either edit the abi2xsf with a text editor of your choice ("vi" for instance) and read the first lines,

or (in the directory where the file is located)  jus type:

./abi2xsf

and you will get:

Usage: abi2xsf [option] abi-out

-c    Convert from bohr to ang (default)

-i    Initial structure 

-f    Final structure (default)

-a    Animation file (initial & final)

-s    Structural Optimization run

Defaults are assumed when no options are provided

So, if you want to have the .xsf of your initial structure you do:

/home/dev/abinit-5.8.4/util/users/abi2xsf    - i  yourfile.out

Best,

Zeila

On 9 Oct 2009, at 20:13, Dev Sharma wrote:

Dear Zeila Sir,
i copied a output file t08.out from v5 directory and run abi2xsf with the following command
/home/dev/abinit-5.8.4/util/users/abi2xsf <t08.out> try.xsf

on which it is giving error as

[dev@dev work_optic]$ sh submit.sh
submit.sh: line 2: /home/dev/abinit-5.8.4/util/users/abi2xsf: Permission denied
even i tried the superuser also
Please advice.
Thanks
Dev,
University of Delhi

On Fri, Oct 9, 2009 at 6:34 PM, Zeila Zanolli <zeila.zanolli@uclouvain.be> wrote:

hi, 

there is also a script in the [your_home_directory_for_abinit]/util/users   called   abi2xsf.

The instructions for using it are writte in the same script  (you can have a look at it with any text editor).

This script needs as input the output of abinit (you don't need to generate the density file).

Then, you can read the .xsf  with Xcrysden.

regards,

Zeila

On 9 Oct 2009, at 14:46, cszakacs@mun.ca wrote:

Hello,

If it is any help, when you run an abinit calculation with the option to create

the density file as well, later on you could use the cut3d to convert the

density file to a file with .xsf extension (Xcrysden format). Now this .xsf

file can be visualized with v_sim or Vesta.

It would be useful to have a graphical interface as well for the creation of the

input file, but I don't know if there is one available. If any other user has

more information about this, I would appreciate if he/she would share it with

us.

Thanks and best regards,

Csaba

Quoting bond james <champbond1983@gmail.com>:

Dear Sir,

In each mail i have written my real name :):)..... Ok sir  i have compile

V_sim in Linux also. But still the same problem is there.

How to open Abinit file in linux. One thing , i have configured the V_sim by

default (./configure).

Thanks Sir,

Dev Sharma,

University of Delhi

On Fri, Oct 9, 2009 at 5:38 PM, Emmanuel Arras <emmanuel.arras@cea.fr>wrote:

I'm afraid the windows version of v_sim doesn't reads abinit inputs.

Regards

Emmanuel

PS: could you change your name (james bond is not very... serious...)

bond james a écrit :

 hi 2 all,

 I have downloaded the v_sim-3.4.4-win32 and extract in. Then in the bin

folder i double click on v_sim. It opens three windows. 1) command panel

2)

another window with title no file loded and 3) command prompt with the

following GtK-Warning with a number of times

<V_sim.exe:524> Gtk-WARNING **: GtkSpinButton : Setting with non zero

page

size is deprecated.

Now when i click on actions--> open (in command panel window) it shows

all

supported formats, but like i have made my file as ZnO.in  name when i

select all file and clcik on ZnO.in , under the preview it makes a

quaetion

mark and says not a v_sim file and give error on opening that wrong XYZ

format

Please help, How to open a Abinit file in the V_sim under Windows.

Thnaks

With regards,

Dev Sharma,

Univeristy of Delhi

India

--

Emmanuel ARRAS

L_Sim (Laboratoire de Simulation Atomistique)

SP2M / INAC

CEA Grenoble

tel : 00 33 (0)4 387 86862

-- 

Csaba Szakacs

Memorial University

Dept. of Chemistry

St. John's, NL

Tel.: 737-6118

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Dr. Zeila Zanolli

Université Catholique de Louvain (UCL)

Unité Physico-Chimie et de Physique des Matériaux (PCPM) 

Place Croix du Sud, 1 (Boltzmann)

B-1348 Louvain-la-Neuve, Belgium

Phone: +32 (0)10 47 3501 

Mobile: +32 (0)487 556699

Fax: +32 (0)10 47 3452

e-mail: zeila.zanolli@uclouvain.be

web: http://www.nano2hybrids.net/

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Dr. Zeila Zanolli

Université Catholique de Louvain (UCL)

Unité Physico-Chimie et de Physique des Matériaux (PCPM) 

Place Croix du Sud, 1 (Boltzmann)

B-1348 Louvain-la-Neuve, Belgium

Phone: +32 (0)10 47 3501 

Mobile: +32 (0)487 556699

Fax: +32 (0)10 47 3452

e-mail: zeila.zanolli@uclouvain.be

web: http://www.nano2hybrids.net/

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