[Pw_forum] Smearing Problem
loc duong ding
mambom1902 at yahoo.com
Wed Jul 1 16:31:50 CEST 2015
Dear Paresh,
Could you try to see the energy evolution of magnetic ordering G and C-type with different smearing value at different k-points mesh? It seems crazy but you may roughly estimate the transition temperature of these two phases based on the electronic temperature. Fermi-Dirac function should be used to reflect the physical meaning of the occupation probability.
Please let me know what you get for that test. I really appreciate to your feedback.
Best regards,
-----------------------------------------------
Dinh Loc Duong , Ph.D
Postdoctoral Researcher, Department of Nanoscience
Max Planck Institute for Solid State Research
Heisenbergstrasse 1, D-70569 Stuttgart, Germany
Email: mambom1902 at yahoo.com, l.duong at fkf.mpg.de
On Wednesday, July 1, 2015 12:01 PM, "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org> wrote:
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Today's Topics:
1. Molecular dynamics (fadwa fad)
2. spin-orbit coupling (Shoutao Zhang)
3. Lowdin charge calculation (Princesse Fadwa)
4. Magnetization (fadwa fad)
5. Re: Magnetization (Giovanni Cantele)
6. projwfc.x crashes when natomwfc iz zero (Jure Varlec)
7. problem -while compiling yambo (chaitanya varma)
8. Re: problem -while compiling yambo (Andrea Ferretti)
9. regarding Graphene nano ribbon (Surender Pratap)
10. Re: projwfc.x crashes when natomwfc iz zero (Paolo Giannozzi)
11. Re: projwfc.x crashes when natomwfc iz zero (Jure Varlec)
12. Spin orbit projwfc error (Rajdeep Banerjee)
13. Re: Smearing Problem (Nicola Marzari)
14. Re: problem -while compiling yambo (chaitanya varma)
----------------------------------------------------------------------
Message: 1
Date: Tue, 30 Jun 2015 12:06:11 +0100
From: fadwa fad <fadwa.me18 at gmail.com>
Subject: [Pw_forum] Molecular dynamics
To: pw_forum at pwscf.org
Message-ID:
<CAMAootd8g8r0QNYTL7xKyUoOR=1Gap2j+_j1TEo2J1i_ZPJpXw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi All,
I need to study the stability of crystal using Molecular dynamics, but I
don't know How can I do it. Can anybody kindly tell me about Molecular
dynamics which I can use for the stability calculation ? Any reply would be
highly appreciated.
Kind regards
Fadwa
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Message: 2
Date: Tue, 30 Jun 2015 19:30:12 +0800 (GMT+08:00)
From: Shoutao Zhang <zst at calypso.cn>
Subject: [Pw_forum] spin-orbit coupling
To: pw_forum <pw_forum at pwscf.org>
Message-ID:
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Dear all,
I would like to know how to take into consideration the spin-orbit coupling (SOC) when calculating the superconducting transition temperature by means of the Quantum ESPRESSO package. May you send the relative input files to me ?
Thanks for your help and I look forward to hearing from you soon.
------------------------------
Message: 3
Date: Tue, 30 Jun 2015 12:52:13 +0100
From: Princesse Fadwa <fadwa.me at live.fr>
Subject: [Pw_forum] Lowdin charge calculation
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Message-ID: <SNT150-W7EDB658E6F9DC6D07504485A90 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi All,I need to know the magnetic moment on each atom. I did the Lowdin charge calculation but I didn't understand the meaning of the results. Any reply would be highly appreciated.Kind regards,Fadwa
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Message: 4
Date: Tue, 30 Jun 2015 13:42:35 +0100
From: fadwa fad <fadwa.me18 at gmail.com>
Subject: [Pw_forum] Magnetization
To: pw_forum at pwscf.org
Message-ID:
<CAMAootcMPKn_VHj5r-AA1fGWCje1oHSTcpVMWAzXGdXhG7Agbw at mail.gmail.com>
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Hi All,
I used system that is not magnetic and I added some dopants to render it
magnetic. My question is How can I know that the system become magnetic or
not with pwscf? and which type of magnetization is it ?
Any help will be highly appreciated.
Kind Regards
Fadwa
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Message: 5
Date: Tue, 30 Jun 2015 14:53:38 +0200
From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
Subject: Re: [Pw_forum] Magnetization
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <D9423EB2-6510-4889-96FC-1318AD0FF95E at spin.cnr.it>
Content-Type: text/plain; charset="us-ascii"
Look through the documentation/tutorials that turn out to be quite helpful to understand basic features of the code.
An example of magnetic calculation is in PW/examples/example01 (see the spin-polarized calculation for nickel).
Also, retrieved for example from http://media.quantum-espresso.org/santa_barbara_2009_07/ <http://media.quantum-espresso.org/santa_barbara_2009_07/> :
http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/MagnCorr.pdf
http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/Handson_lsda.pdf <http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/Handson_lsda.pdf>
As you will see, you must use the variables nspin and starting_magnetization to drive the system out of the local, spin-unpolarised minimum.
If your system is magnetic, the output file will show you final values of the total and/or absolute magnetisation different from zero.
GIOVANNI
> On 30 Jun 2015, at 14:42, fadwa fad <fadwa.me18 at gmail.com> wrote:
>
> Hi All,
>
> I used system that is not magnetic and I added some dopants to render it magnetic. My question is How can I know that the system become magnetic or not with pwscf? and which type of magnetization is it ?
> Any help will be highly appreciated.
>
> Kind Regards
> Fadwa
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74
ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
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Message: 6
Date: Tue, 30 Jun 2015 15:40:35 +0200
From: Jure Varlec <jure.varlec at ki.si>
Subject: [Pw_forum] projwfc.x crashes when natomwfc iz zero
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <20150630154035.2e758497 at ki.si>
Content-Type: text/plain; charset="US-ASCII"
Dear all,
I have run into a situation where projwfc.x crashes with error
On entry to ZHEEV parameter number 5 had an illegal value
This issue was reported about a year ago, but the poster never followed
through with more information. I have tracked the error down to the
basis::natomwfc variable, which for some reason is zero. Looking at
data-file.xml from the scf run, NUMBER_OF_ATOMIC_WFC is, in fact, zero.
This happens when the scf is done using sg15_oncv norm-conserving
pseudopotentials, but not when using GBRV ultrasoft pseudopotentials;
apart from ecut{wfc,rho}, everything is the same. How to proceed?
A related question. Not being very familiar with fortran, finding my
way around QE code is tedious. I could not figure out where
basis::natomwfc is actually set. I tried to use gdb watchpoints on the
__basis_MOD_natomwfc symbol, which is what gfortran produces. While the
read watchpoint got tripped many times as this variable is used quite a
lot, the write watchpoint was never tripped, implying that this
variable is not set at all, which I find very strange. However, the
watchpoint was tripped in qexml_module::qexml_read_bands_info when
data-file.xml was produced using GBRV pseudopotentials. To me, this
looks like NC pseudopotentials don't use natomwfc, but surely this
can't be, this variable is used all over the place. Are watchpoints on
global variables in fortran realiable at all?
My ignorance of the inner workings of QE now being obvious :) , I hope
the above information will be of some use for finding the problem.
Best regards,
Jure Varlec
------------------------------
Message: 7
Date: Tue, 30 Jun 2015 14:11:01 +0000 (UTC)
From: chaitanya varma <chvar81 at yahoo.co.in>
Subject: [Pw_forum] problem -while compiling yambo
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<448700113.1698796.1435673461491.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"
HiI am new to espressoi installed espress-5.2 and tried to do make yambobut i am getting error
[Making slatec]<<<
make[3]: Entering directory `$/espresso-5.2.0/yambo-3.4.1-rev61/lib/slatec'
Makefile:70: *** missing separator.? Stop.
please let me know how to overcome this problem
regards
?Chaitanya Varma M ?
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Message: 8
Date: Tue, 30 Jun 2015 16:38:15 +0200 (CEST)
From: Andrea Ferretti <andrea.ferretti at unimore.it>
Subject: Re: [Pw_forum] problem -while compiling yambo
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <alpine.DEB.2.10.1506301637400.18427 at potzie>
Content-Type: text/plain; charset="utf-8"
Dear Chaitanya,
this issue is normally related to the c-precompiler (which is used to produce a
bit entering the makefile system of yambo).
can you send the make.sys file generated by the configuration of QE ?
usually it is enough to change some flags there and the problem is sorted out
BTW:
this issue is partly discussed at the link below for the direct (self-standing)
configuration/compilation of yambo
http://www.yambo-code.org/forum/viewtopic.php?f=1&t=300
Andrea
> Hi
> I am new to espresso
> i installed espress-5.2 and tried to do make yambo
> but i am getting error
> [Making slatec]<<<
> make[3]: Entering directory `$/espresso-5.2.0/yambo-3.4.1-rev61/lib/slatec'
> Makefile:70: *** missing separator.? Stop.
>
> please let me know how to overcome this problem
>
> regards
> ?
> Chaitanya Varma M
> ?
>
>
--
Andrea Ferretti, PhD
S3 Center, Istituto Nanoscienze, CNR
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it
------------------------------
Message: 9
Date: Tue, 30 Jun 2015 20:16:00 +0530
From: Surender Pratap <suren1986dhalaria at gmail.com>
Subject: [Pw_forum] regarding Graphene nano ribbon
To: PWSCF Forum <Pw_forum at pwscf.org>
Message-ID:
<CAF+T5enRj9c6nFipC0mLXay5Jzc8eTHNzYHEZ=XSy2c9jf4qgA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all users
I am simulating GNR,with the help of matlab,and in results i am getting
self energies in complex forms,can any body tell me if some one has worked
in this area,why these broadening as well as self energy matrices are
coming in complex forms,or any one has simulated through Quantum Espresso
GNR,what kind of shape they have got for conductance ,LDOS .This is the
case of without magnetic field term or electric field term,and my hopping
terms are simply a number not in terms of vector potential.I am stuck off
at this point ,please let me know what else i can do?
regards
Surender Pratap
Research Scholar
Physics Department
BITS Pilani,Pilani Campus Rajsthan-333031(INDIA)...
Mob-7891949445
*Birla Institute of Technology & Science,* Pilani
Pilani 333031, Rajasthan, India
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Message: 10
Date: Tue, 30 Jun 2015 17:04:50 +0200
From: Paolo Giannozzi <p.giannozzi at gmail.com>
Subject: Re: [Pw_forum] projwfc.x crashes when natomwfc iz zero
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CAPMgbCtELGuqKbpf4shRbiHK5C6jzwG_ZCU3XLij7MS3ztk+dQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
On Tue, Jun 30, 2015 at 3:40 PM, Jure Varlec <jure.varlec at ki.si> wrote:
> I have run into a situation where projwfc.x crashes with error
>
> On entry to ZHEEV parameter number 5 had an illegal value
>
> [...] I have tracked the error down to the basis::natomwfc variable, which
> for some reason is zero
it is (I guess but I am quite sure) for a very specific reason: there are
no atomic wavefunctions. These are read from pseudopotential files, but not
all PP files contain them. Most computations do not use, or anyway do not
require, them. Projection on atomic wavefunctions, of course, requires at
least one of them.
> This happens when the scf is done using sg15_oncv norm-conserving
> pseudopotentials, but not when using GBRV ultrasoft pseudopotentials; apart
> from ecut{wfc,rho}, everything is the same
>
See above
A related question. Not being very familiar with fortran, finding my way
> around QE code is tedious.
it is even if you are very familiar with fortran
> I could not figure out where basis::natomwfc is actually set
For calculations performed by pw.x, in PW/src/setup.f90, line 355:
natomwfc = n_atom_wfc( nat, ityp, noncolin )
Other executables read it from file (routine qexml_read_bands_info)
To me, this looks like NC pseudopotentials don't use natomwfc, but surely
> this
> can't be, this variable is used all over the place.
See above: it is useful (but not needed) to start self-consistency and
iterative diagonalization; it is required by DFT+U, by projection over
atomic wavefunctions, by projected DOS, and likely in a few more cases
> My ignorance of the inner workings of QE now being obvious :)
I beg to disagree: you were able to track an error to its cause
Paolo
--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Message: 11
Date: Tue, 30 Jun 2015 17:56:29 +0200
From: Jure Varlec <jure.varlec at ki.si>
Subject: Re: [Pw_forum] projwfc.x crashes when natomwfc iz zero
To: <pw_forum at pwscf.org>
Message-ID: <20150630175629.7c6ea358 at ki.si>
Content-Type: text/plain; charset="US-ASCII"
On Tue, 30 Jun 2015 17:04:50 +0200
Paolo Giannozzi <p.giannozzi at gmail.com> wrote:
> it is (I guess but I am quite sure) for a very specific reason: there
> are no atomic wavefunctions. These are read from pseudopotential
> files, but not all PP files contain them. Most computations do not
> use, or anyway do not require, them. Projection on atomic
> wavefunctions, of course, requires at least one of them.
I see. Looking at the UPF file, it does say has_wfc="F"; now I know
what it means. So I'm off to find another program to generate
pseudopotentials using libxc (I wish to experiment with van der Waals
functionals). Suggestions welcome :)
Thank you very much for a quick and concise explanation.
Best regards
Jure
------------------------------
Message: 12
Date: Wed, 1 Jul 2015 10:49:16 +0530
From: Rajdeep Banerjee <rajdeep.jzs at gmail.com>
Subject: [Pw_forum] Spin orbit projwfc error
To: pw_forum at pwscf.org
Message-ID:
<CA+YfB7QGpqiGYyp8fWA6yWqSyEUYfqROLZ9kbS4iR0p0GO5bMw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all,
I was trying to run projected density of states from an nscf
calculation with spin-orbit included and I am getting the following error:
Calling projwave_nc ....
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine d_matrix_so (5):
D_S (j=1/2) for this symmetry operation is not unitary
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
I am running it on espresso-5.0.1 and I am attaching the scf,
nscf and pdos inputs so that one can reproduce the error.
Please help me if anyone has any idea on how to resolve the
issue.
(as far as I know the previous discussions on this issue in pw_forum
doesn't reach any conclusive result. So I am asking again. Very sorry for
repitition)
Thanks amd regards,
--
Rajdeep Banerjee
PhD student
JNCASR, Bangalore
India
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Message: 13
Date: Wed, 01 Jul 2015 15:26:43 +0800
From: Nicola Marzari <nicola.marzari at epfl.ch>
Subject: Re: [Pw_forum] Smearing Problem
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <55939633.9090403 at epfl.ch>
Content-Type: text/plain; charset=windows-1252; format=flowed
Dear Paresh,
maybe this is easier to follow:
http://theossrv1.epfl.ch/Main/ElectronicTemperature
The main concept is that with very small smearing you need *a lot* of
k-points
to perform the correct Brillouin zone integrations - so with a 0.00184
smearing
you have a *large* error due to insufficient sampling, not a small error.
Solution 1 - if you do not want to think, ever, in your life, use 0.01
Ry of m-v
or m-v smearing, and increase the k-point sampling until the difference
in energy
between G and C type is converged.
Solution 2 - plot the energy difference between G and C as a function of
smearing,
for m-v smearing of 0.005, 0.010, 0.015, 0.020, 0.025, and with at least
3 or
4 k-point sampling. Use the discussion from
http://theossrv1.epfl.ch/Main/ElectronicTemperature
to understand what to do.
nicola
On 30/06/2015 17:07, paresh rout wrote:
> Dear all,
> I am dealing with a transition metal oxide compound (ABO3), Where I use
> cold smearing *m-v(0.02)* for geometry optimization and for total energy
> calculation I use *f-d (0.00184*) at the final optimized structure. I
> have calculated the total energy for various type of magnetic ordering
> like (G-type, C-type). The total energy (SCF) for G-type and C-type are
> in reverse ordering for different smearing technique (*G-type is the
> ground state for* *MV smearing and C-type is the ground state for FD*).
> But when I reduced the value of degauss of *MV to 0.008 *I got the same
> ordering as FD.
> I am very confused about the smearing technique . I have also read Prof.
> Nicola's thesis about smearing but there I did not get rid of my
> confusion also I did not find about FD technique . Can anybody kindly
> tell me about the right smearing technique which I can use for the spin
> polarized calculation ? Any reply would be highly appreciated.
>
>
> Kind Regards
> Paresh Chandra Rout
> Research Scholar
> INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH, BHOPAL
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
------------------------------
Message: 14
Date: Wed, 1 Jul 2015 07:27:45 +0000 (UTC)
From: chaitanya varma <chvar81 at yahoo.co.in>
Subject: Re: [Pw_forum] problem -while compiling yambo
To: "andrea.ferretti at unimore.it" <andrea.ferretti at unimore.it>, PWSCF
Forum <pw_forum at pwscf.org>
Message-ID:
<2049072337.188256.1435735665329.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"
thank youi am sending make.sys file which was generated when i compiled espress-5.2rregards?Chaitanya Varma M ?
On Tuesday, 30 June 2015 8:08 PM, Andrea Ferretti <andrea.ferretti at unimore.it> wrote:
Dear Chaitanya,
this issue is normally related to the c-precompiler (which is used to produce a
bit entering the makefile system of yambo).
can you send the make.sys file generated by the configuration of QE ?
usually it is enough to change some flags there and the problem is sorted out
BTW:
this issue is partly discussed at the link below for the direct (self-standing)
configuration/compilation of yambo
http://www.yambo-code.org/forum/viewtopic.php?f=1&t=300
Andrea
> Hi
> I am new to espresso
> i installed espress-5.2 and tried to do make yambo
> but i am getting error
> [Making slatec]<<<
> make[3]: Entering directory `$/espresso-5.2.0/yambo-3.4.1-rev61/lib/slatec'
> Makefile:70: *** missing separator.? Stop.
>
> please let me know how to overcome this problem
>
> regards
> ?
> Chaitanya Varma M
> ?
>
>
--
Andrea Ferretti, PhD
S3 Center, Istituto Nanoscienze, CNR
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322;? Skype: andrea_ferretti
URL: http://www.nano.cnr.it
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
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