[ase-users] ase-users Digest, Vol 56, Issue 6

Thu Feb 7 11:29:54 CET 2013

Hello Sungsik Kim 

I used Opensuse 12.1 

Before this error which
library you're compiling, you wrote in the previous email.
For export we
did everything you're doing without the user root using sudo.

Dacapo
recommend deleting the folder and redo again instead of compile errors.

In the folder dacapo/ src you try. 

sudo -s (root mode)

make
gfortran_fsecond_underscore 

Regards 

Fábio 

Em 07.02.2013 02:29,
ase-users-request at listserv.fysik.dtu.dk escreveu: 

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> 1. Re:
ase-users Digest, Vol 56, Issue 5 (Sungsik Kim)
> 2. Re:
ASE.UTILS.GEOMETRY question (Jens J?rgen Mortensen)
> 3. Re:
ASE.UTILS.GEOMETRY question (Jens J?rgen Mortensen)
> 
>
----------------------------------------------------------------------
>

> Message: 1
> Date: Wed, 6 Feb 2013 03:56:25 -0800
> From: Sungsik Kim
<sungsik312 at gmail.com>
> Subject: Re: [ase-users] ase-users Digest, Vol
56, Issue 5
> To: ase-users at listserv.fysik.dtu.dk
> Message-ID:
>
<CAKEEm2iNCh-5NsFQTWeEyMfa80kiOcLkt3mqasuCZ2Zz6AqZ1w at mail.gmail.com>
>
Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello, Fabio.
Thanks
> 
> I checked the version of gfortran by gfortran -v.
> 
> The
version installed is gcc version 4.7.2.
> 
> It there any way to install
dacapo on gcc version 4.7.2 ?
> 
> I try to downgrade gcc version to
4.2.1 on Ubuntu 12.10.
> 
> It does not work to me on my computer.
> 
>
Thanks again
> 
> 2013/2/6 <ase-users-request at listserv.fysik.dtu.dk>
>

>> Send ase-users mailing list submissions to
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World Wide Web, visit
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Contents of ase-users digest..." Today's Topics: 1. Re: ase-users
Digest, Vol 56, Issue 4 (fabio.lima)
----------------------------------------------------------------------
Message: 1 Date: Tue, 05 Feb 2013 16:43:43 -0400 From: "fabio.lima"
<fabio.lima at ufms.br> Subject: Re: [ase-users] ase-users Digest, Vol 56,
Issue 4 To: <ase-users at listserv.fysik.dtu.dk> Message-ID:
<982ada732b4eb59fc103c94d0230c95b at ufms.br> Content-Type: text/plain;
charset="utf-8" Hello Maybe is the build versions of gfortran, see which
version of the compilation gfotran-v is good gfortran < 4.6 Cheers Fabio
Em 05.02.2013 07:00,
ase-users-request at listserv.fysik.dtu.dkescreveu:Send ase-users mailing
list submissions toase-users at listserv.fysik.dtu.dk 
>> 
>>> To subscribe
or unsubscribe via the
>> World Wide Web,
visithttps://listserv.fysik.dtu.dk/mailman/listinfo/ase-users [1][1] 
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>>> or, via
>> email, send a message with subject or body 'help'
toase-users-request at listserv.fysik.dtu.dk
ase-users-owner at listserv.fysik.dtu.dk WhenSubject: [ase-users]
Installation of ASE-DACAPO On Ubuntu 12.10
CAKEEm2gYGZzV7wP32ByCvR=vfr15S6iCx1hze5N9JdBOW60+pw at mail.gmail.com>Content-Type:
text/plain; charset="iso-8859-1" I am installing dacapo on Ubuntu
12.10. I am a newer to Ubuntu. make[2]: Leaving directory
`/home/sungsik/dacapo/src/gfortran_fsecond_underscore_ser
>> 
>>>
100%">make[1]:
>> rial] Error 2 make
>> 
>>> 5px; border-left:#1010f
>>
margin-left:5px; width:100%">make: *** [gfortran_fsecond_underscore]
Error
2#######################################################################################################
Here is my procedure to install dacapo. sudo apt-g
>> 
>>> 2px solid;
margin-left:5px; width:100%">sudo apt-
>> ibnetcdf-dev sudo apt-get
install netcdf-bin sudo apt-get install gfortran sudo apt-get install
python-scienti
>> 
>>> 00%">sudo apt-get install
>> t-get install rasmol
sudo apt-get install gnuplot sudo apt-get install pyth
>> 
>>>
width:10
>> get install python-vtk sudo apt-get install
python-matplotlib https://svn.fysik.dtu.dk/projects/ase/trunk[2] ase svn
co https://svn.fysik.dtu.dk/projects/dacapo/trunk [2][3] dacapo cp -pr
dacapo/psp/*/*/*.pseudo psp export NETCDF="/usr/lib"
PYTHONPATH=${HOME}/dacapo/Python:${HOME}/ase
------------------------------
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> ------------------------------
> 
> Message: 2
> Date: Thu, 7
Feb 2013 07:25:48 +0100
> From: Jens J?rgen Mortensen
<jensj at fysik.dtu.dk>
> Subject: Re: [ase-users] ASE.UTILS.GEOMETRY
question
> To: "S. Sanchez" <lcqsigi at gmail.com>
> Cc:
ase-users at listserv.fysik.dtu.dk
> Message-ID:
<511348EC.9000608 at fysik.dtu.dk>
> Content-Type: text/plain;
charset="iso-8859-1"
> 
> Den 01-02-2013 11:49, S. Sanchez skrev:
> 
>>
Dear ASE users, I have a rather simple question, regarding the
"ase.utils.geometry" module. I was able to construct a (111) surface out
of a crystalline system that contains 2 different atoms. Now, I want to
know how can I control the beginning/termination of my surface. That is,
if I want the first and last layers of my slab to have the same type of
atoms, how can I do that? Could you please advice? After running my
script, I got the following 6-layer slab: layer-1 Atom_A layer-2 Atom_B
layer-3 Atom_B layer-4 Atom_A layer-5 Atom_B layer-6 Atom_B However, I'd
like to have something like this: layer-1 Atom_B layer-2 Atom_A layer-3
Atom_B layer-4 Atom_B layer-5 Atom_A layer-6 Atom_B
> 
> Maybe you can
just make a thick slab and then cut off what you don't need:
> 
> del
atoms[atoms.positions[:, 2] > 23.4]
> del atoms[atoms.positions[:, 2] <
12.3]
> 
> (atoms.positions[:, 2] are the z-coordinates of your atoms)
>

> Jens J?rgen
> Best, SS
_______________________________________________ ase-users mailing list
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> ------------------------------
> 
> Message: 3
> Date: Thu, 7
Feb 2013 07:28:39 +0100
> From: Jens J?rgen Mortensen
<jensj at fysik.dtu.dk>
> Subject: Re: [ase-users] ASE.UTILS.GEOMETRY
question
> To: "S. Sanchez" <lcqsigi at gmail.com>
> Cc:
ase-users at listserv.fysik.dtu.dk
> Message-ID:
<51134997.4030904 at fysik.dtu.dk>
> Content-Type: text/plain;
charset="iso-8859-1"
> 
> Den 01-02-2013 15:13, S. Sanchez skrev:
> Dear
ASE users, After creating a (111) surface using ASE.UTILS.GEOMETRY; I
end up with a simulation cell, whose unit-cell axes are larger than
needed. Is there a way to reduce the resulting unit cell-axes dimensions
automatically, while keeping the symmetry of cell? 
> 
> Try the
surface() function:
> 
>
https://wiki.fysik.dtu.dk/ase/ase/surface.html#create-specific-non-common-surfaces
[5]Jens J?rgen
> Thanks, SS
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> End of
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>
****************************************
> 
>> 
> 
>> 
> 
>> 

--

Fábio de Lima
Chemistry Department - UFMS
Phone: 55 (67)
3345-3596
Cellular: 55 (67) 9639-1338

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[5]
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