[Pw_forum] How to start and use QE open source simulation

Naol Regassa greatnaol at gmail.com
Thu Jun 18 13:56:37 CEST 2009


Hello Yosef

You can get the file for QE and XcrysDen from AAU, Materials science
programe (Room 111). Try contact us when you come to Addis. We may
help you on how to install, configure and start up.

Tamene Regassa
Student at AAU,
Materials science programe

On 6/17/09, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
>
>    1. Re: File closing errors when using NEB image	parallelization
>       (J. J. Ramsey)
>    2. Re: How to start and use QE open source simulation
>       (Nicola Marzari)
>    3. Re: How to start and use QE open source simulation
>       (Giovanni Cantele)
>    4. Re: Elastic Constant. (Huiqun Zhou)
>    5. Re: Elastic Constant. (Huiqun Zhou)
>    6. Re: Elastic Constant. (Huiqun Zhou)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 16 Jun 2009 09:04:27 -0700 (PDT)
> From: "J. J. Ramsey" <jjr19 at uakron.edu>
> Subject: Re: [Pw_forum] File closing errors when using NEB image
> 	parallelization
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <419763.82623.qm at web50910.mail.re2.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> ----- Original Message ----
>
>> If I had to bet I would say you are using ~/tmp as the default directory,
>>
>> and it is a normal NFS share.
>
> Actually, it's a subdirectory under /usr/var/tmp, and to the best of my
> knowledge, it is not an NFS share. There is a bit more info, here:
> http://www.arl.hpc.mil/Systems/mjm_docs.html#fs
>
> Also, I had even tried out my problem on an entirely different cluster which
> uses the Parallel File System
> (http://www.osc.edu/supercomputing/computing/pvfs/index.shtml) and got the
> same problems.
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 16 Jun 2009 12:27:07 -0400
> From: Nicola Marzari <marzari at MIT.EDU>
> Subject: Re: [Pw_forum] How to start and use QE open source simulation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4A37C7DB.1030803 at mit.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> yoseph Getachew wrote:
>> Dear All ,
>>
>> sorry but this is a very low level question.
>>
>> would you please inform me as to how i can install,configure, and make
>> all the necessary steps so that i can be able to run simulations. i
>> have tried to use the QE website but i ended up in so much more
>> inconsistencies.
>>
>> for example where and how  can i get and install fortan and c.xcrysden
>> which binary or static files should i use  and how should i install them.
>>
>> i need your specific advise on this to catch up with everybody.
>>
>> Regards,
>> Yoseph Getachew
>> ArbaMinch University,
>> Department of Physics
>
>
> Hi Yoseph,
>
> it looks like you need to start with some basics on Linux. Do you
> have anyone familiar with that in the Department, or can you access
> some online guide ? People might have better suggestions here.
>
> At a minimum, to install Quantum ESPRESSO you need a Fortran compiler,
> and (I think) a C compiler. The Intel fortran and c compilers are very
> efficient, but would need to be downloaded from the Intel site (I have
> left a copy of those at Addis Abeba, not sure if it is still there -
> contact SibKrishna Ghoshal <lordshib at gmail.com>).
>
> gfortran and gcc would be standard alternatives, available from many
> Linux distributions.
>
> 			nicola
>
>
>
> --
> ---------------------------------------------------------------------
> Prof Nicola Marzari   Department of Materials Science and Engineering
> 13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
> tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 16 Jun 2009 18:27:25 +0200
> From: Giovanni Cantele <Giovanni.Cantele at na.infn.it>
> Subject: Re: [Pw_forum] How to start and use QE open source simulation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4A37C7ED.5060305 at na.infn.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> yoseph Getachew wrote:
>> Dear All ,
>>
>> sorry but this is a very low level question.
>>
>> would you please inform me as to how i can install,configure, and make
>> all the necessary steps so that i can be able to run simulations. i
>> have tried to use the QE website but i ended up in so much more
>> inconsistencies.
>>
> actually, it is rather hard to help you, due to loss of information.
> Which kind of inconsistencies? In compiling QE? At run time?
> It seems to me that lot of information can be found here:
> http://www.quantum-espresso.org/wiki/index.php/Installation
> there are also compiler/architecture-related issues mentioned there.
> The user guide is also reported within the distribution
> (Doc/user_guide.html).
>> for example where and how  can i get and install fortan and c.
> on which system? Do you have a Linux distribution? Maybe ubuntu?
> I've the Intel fortran/C compiler that I freely downloaded from the
> Intel web site,
> I guest it is still free.
> Another possibility is gfortran, I would install it on my PC using
> sudo apt-get install gfortran
> but a different command is needed for other linux distributions.
>> xcrysden
>> which binary or static files should i use  and how should i install them.
>>
> are you sure that what reported on the web site is useless for you?
> Go to (did you already do it?)
> http://www.xcrysden.org/doc/install.html
> I find many sections:
> *Installation Instructions
> <http://www.xcrysden.org/doc/install.html#__toc__0>*
>     */How to Install the Compiled Package
> <http://www.xcrysden.org/doc/install.html#__toc__1>/*
>         /FOR IMPATIENT: minimal installation instructions
> <http://www.xcrysden.org/doc/install.html#__toc__2>/
>         /A Bit Longer Installation Instructions
> <http://www.xcrysden.org/doc/install.html#__toc__3>/
>         /What xcConfigure does?
> <http://www.xcrysden.org/doc/install.html#__toc__4>/
>     */How to Install the Source Package
> <http://www.xcrysden.org/doc/install.html#__toc__5>/*
>         /Trouble Shooting
> <http://www.xcrysden.org/doc/install.html#__toc__6>/
>
> Someone also had the patience to suggest installation instructions for both
> impatient and patient users!!!!!
> Did you follow all the suggested steps, and in case which was the one
> failing?
>
>> i need your specific advise on this to catch up with everybody.
>>
>> Regards,
>> Yoseph Getachew
>> ArbaMinch University,
>> Department of Physics
>>
>>
>>
>
> Best regards,
>
>     Giovanni
>
> --
>
>
>
> Dr. Giovanni Cantele
> Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario di Monte S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910
> Fax:   +39 081 676346
> E-mail: giovanni.cantele at cnr.it
>         giovanni.cantele at na.infn.it
> Web: http://people.na.infn.it/~cantele
> Research Group: http://www.nanomat.unina.it
> Skype contact: giocan74
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 17 Jun 2009 15:05:37 +0800
> From: "Huiqun Zhou" <hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] Elastic Constant.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <A496B90FFCD3402F9560CE84F4D17CFC at RAPIDMIND>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> Stefano,
>
> The straightforward approach is tedious for orthorgonal, monolinic, trilinic
> systems. Should the lost implementation gain in these respects?
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
> ----- Original Message -----
> From: "Stefano Baroni" <baroni at sissa.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Sunday, June 14, 2009 6:01 PM
> Subject: Re: [Pw_forum] Elastic Constant.
>
>
>> Dear Bipul,
>>
>> long ago there used to be an implementation of the linear-response
>> approach to elastic constants by SB, Giannozzi, and Testa:
>> % Copyright (C) 2009 The American Physical Society
>> % Please report any problems to prola at aps.org
>>
>> @Article{PhysRevLett.59.2662,
>>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>>   journal = {Phys. Rev. Lett.},
>>   volume = {59},
>>   number = {23},
>>   pages = {2662--2665},
>>   numpages = {3},
>>   year = {1987},
>>   month = {Dec},
>>   doi = {10.1103/PhysRevLett.59.2662},
>>   publisher = {American Physical Society}
>> }
>> This is no longer available, partly because of the programmers'
>> lazyness, partly because there is not much to be gained with respect
>> to the straightforward approach you are following.
>>
>> Stefano B
>>
>>
>> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
>>
>>> Dear Pwscf user,
>>> I want to calculate the elastic constants for cubic structure for
>>> LaSb, which is having NaCl structure. Although I have written a small
>>> script for doing that. But if anybody develop any code, do he/she like
>>> to share, so that I can compare my results.
>>> Thanks
>>> --
>>> Bipul Rakshit
>>> PhD Student,
>>> Barkatullah University,
>>> Bhopal 462026,
>>> MP, India
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 17 Jun 2009 14:36:39 +0800
> From: "Huiqun Zhou" <hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] Elastic Constant.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <B8F67D2B4DF543E3B6A8B413A92F7BA2 at RAPIDMIND>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> Stefano,
>
> The straightforward approach is tedious for orthorgonal, monolinic, trilinic
> systems. Should the lost implementation gain in these respects?
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
> ----- Original Message -----
> From: "Stefano Baroni" <baroni at sissa.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Sunday, June 14, 2009 6:01 PM
> Subject: Re: [Pw_forum] Elastic Constant.
>
>
>> Dear Bipul,
>>
>> long ago there used to be an implementation of the linear-response
>> approach to elastic constants by SB, Giannozzi, and Testa:
>> % Copyright (C) 2009 The American Physical Society
>> % Please report any problems to prola at aps.org
>>
>> @Article{PhysRevLett.59.2662,
>>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>>   journal = {Phys. Rev. Lett.},
>>   volume = {59},
>>   number = {23},
>>   pages = {2662--2665},
>>   numpages = {3},
>>   year = {1987},
>>   month = {Dec},
>>   doi = {10.1103/PhysRevLett.59.2662},
>>   publisher = {American Physical Society}
>> }
>> This is no longer available, partly because of the programmers'
>> lazyness, partly because there is not much to be gained with respect
>> to the straightforward approach you are following.
>>
>> Stefano B
>>
>>
>> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
>>
>>> Dear Pwscf user,
>>> I want to calculate the elastic constants for cubic structure for
>>> LaSb, which is having NaCl structure. Although I have written a small
>>> script for doing that. But if anybody develop any code, do he/she like
>>> to share, so that I can compare my results.
>>> Thanks
>>> --
>>> Bipul Rakshit
>>> PhD Student,
>>> Barkatullah University,
>>> Bhopal 462026,
>>> MP, India
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 17 Jun 2009 15:02:09 +0800
> From: "Huiqun Zhou" <hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] Elastic Constant.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <B908FC1250F64DCBB07A974126733A61 at RAPIDMIND>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> Stefano,
>
> The straightforward approach is tedious for orthorgonal, monolinic, trilinic
> systems. Should the lost implementation gain in these respects?
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
> ----- Original Message -----
> From: "Stefano Baroni" <baroni at sissa.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Sunday, June 14, 2009 6:01 PM
> Subject: Re: [Pw_forum] Elastic Constant.
>
>
>> Dear Bipul,
>>
>> long ago there used to be an implementation of the linear-response
>> approach to elastic constants by SB, Giannozzi, and Testa:
>> % Copyright (C) 2009 The American Physical Society
>> % Please report any problems to prola at aps.org
>>
>> @Article{PhysRevLett.59.2662,
>>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>>   journal = {Phys. Rev. Lett.},
>>   volume = {59},
>>   number = {23},
>>   pages = {2662--2665},
>>   numpages = {3},
>>   year = {1987},
>>   month = {Dec},
>>   doi = {10.1103/PhysRevLett.59.2662},
>>   publisher = {American Physical Society}
>> }
>> This is no longer available, partly because of the programmers'
>> lazyness, partly because there is not much to be gained with respect
>> to the straightforward approach you are following.
>>
>> Stefano B
>>
>>
>> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
>>
>>> Dear Pwscf user,
>>> I want to calculate the elastic constants for cubic structure for
>>> LaSb, which is having NaCl structure. Although I have written a small
>>> script for doing that. But if anybody develop any code, do he/she like
>>> to share, so that I can compare my results.
>>> Thanks
>>> --
>>> Bipul Rakshit
>>> PhD Student,
>>> Barkatullah University,
>>> Bhopal 462026,
>>> MP, India
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 24, Issue 35
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