From venkyphysicsiitm at gmail.com Tue Feb 4 11:05:30 2014 From: venkyphysicsiitm at gmail.com (venkatesh chandragiri) Date: Tue, 4 Feb 2014 15:35:30 +0530 Subject: [xcrysden] error in installation and unable to open the case.struct file Message-ID: Sir, i have successfully installed the recent xcrysden-semi-shared one. But while i am running, it is prompting a error saying that error while sharing the libraries: libqudmath.so.0: can not open shared object file: No such file or directory. May be due to this i could not able to open any case.struct file from the Wien2k working directory. please help me to install the this library Further, i have also installed wien2k in the same system but i can not able to see the "view structure option" in the w2web format of wien2k. How could i add this option to my Wien2k programme in w2web. thanks in advance. regards, Ch. Venkatesh, C/o. Prof. V. Srinivas, Department of Physics IIT chennai ph: +91445909693 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140204/56db643c/attachment.htm From tone.kokalj at ijs.si Thu Feb 6 15:37:44 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 06 Feb 2014 15:37:44 +0100 Subject: [xcrysden] error in installation and unable to open the case.struct file In-Reply-To: References: Message-ID: <1391697464.26403.28.camel@catalyst.ijs.si> On Tue, 2014-02-04 at 15:35 +0530, venkatesh chandragiri wrote: > > Sir, > > > i have successfully installed the recent xcrysden-semi-shared one. But > while i am running, it is prompting a error saying that error while > sharing the libraries: libqudmath.so.0: can not open shared object > file: No such file or directory. It's because your system lacks the libquadmath library. The easiest is to install the corresponding package from your linux distro that provides this library. E.g., for Debian based distros (as root or sudo): apt-get install libquadmath0 For RedHat/Fedora based distro (probably): yum install libquadmath0 (if this does not work, try: yum whatprovides libquadmath) Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From vnegi at students.iiserpune.ac.in Tue Feb 11 09:44:49 2014 From: vnegi at students.iiserpune.ac.in (Vikas Negi) Date: Tue, 11 Feb 2014 14:14:49 +0530 Subject: [xcrysden] Error visualizing MD output Message-ID: Hi all, I am trying to open a pwscf output file (from a md run) in Xcrysden-1.5.24. I keep getting the following error message: pwo2xsf.sh: 306: bc: not found What does it mean and how can I resolve this problem? Kindly help! Regards, Vikas Negi Shell Technology Centre Bangalore, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140211/7305d034/attachment.htm From tone.kokalj at ijs.si Tue Feb 11 09:52:33 2014 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 11 Feb 2014 09:52:33 +0100 Subject: [xcrysden] Error visualizing MD output In-Reply-To: References: Message-ID: <1392108753.4377.1.camel@catalyst.ijs.si> On Tue, 2014-02-11 at 14:14 +0530, Vikas Negi wrote: > Hi all, > > > I am trying to open a pwscf output file (from a md run) in > Xcrysden-1.5.24. I keep getting the following error message: > > > pwo2xsf.sh: 306: bc: not found You do not have the "bc" calculator installed on your computer (pwo2xsf.sh script uses it). Depending on your linux distro, you may install it as apt-get install bc (for Debian based systems) or yum install bc (for Fedora based systems) Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From member at linkedin.com Thu Feb 20 10:44:14 2014 From: member at linkedin.com (Acharya 4689 via LinkedIn) Date: Thu, 20 Feb 2014 09:44:14 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_no_LinkedIn=3F?= Message-ID: <20178940.11559419.1392889454178.JavaMail.app@ela4-app0046.prod> LinkedIn ------------ Acharya 4689 solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de Acharya 4689 http://www.linkedin.com/e/-fe5rcs-hrvuf1az-18/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I548937007_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnPsMc3sPejwQdkALs6Ffsk55hzgLc3gUdP8Tc3oOc38LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=1vYiyd89LEeC81 Visualizar perfil de Acharya 4689 http://www.linkedin.com/e/-fe5rcs-hrvuf1az-18/rso/62314166/U7OM/name/128644874_I548937007_125/?hs=false&tok=2mwqiMJKjEeC81 ------------------------------------------ Voc? est? recebendo e-mails de convites. Este e-mail era para Andr? Pereira XCrysden. Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hrvuf1az-18/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2FE5oXYDTEeC81 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140220/886792d9/attachment.htm From cristalmir70 at yahoo.fr Fri Feb 21 14:00:12 2014 From: cristalmir70 at yahoo.fr (mir ali) Date: Fri, 21 Feb 2014 13:00:12 +0000 (GMT) Subject: [xcrysden] (no subject) Message-ID: <1392987612.21345.YahooMailNeo@web172302.mail.ir2.yahoo.com> 41.111.75.232 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20140221/6a9f7d46/attachment.htm From bogus@does.not.exist.com Mon Feb 24 10:28:22 2014 From: bogus@does.not.exist.com () Date: Mon, 24 Feb 2014 09:28:22 -0000 Subject: No subject Message-ID:

XCrySDen can build simple {N}x{M}x{K} type of supercells.
To correctly extract the atoms within the supercell do the following:

1. generate the supercell via menu: Modify-->Number of units drawn

2. change unit of repetition to translational asymmetric unit via menu
Display-->Unit of repetition ...-->Translation asymmetric unit

3, save the XSF file via: File-->Save XSF structure

Then in the so generated file the atoms within the supercell are printed in the "ATOMS" section.


However I have not been able to apply my findings to my work. I used cygwin= as a platform for QE calculations and I have xcrysden installed.
I will really appreciate any comment that will help me resolve this.
Thank you all.


Akemu Rita
UNIBEN
Nigeria.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/= pipermail/xcrysden/attachments/20140430/9b23f912/attachment.html

------------------------------

_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden


End of XCrySDen Digest, Vol 76, Issue 1
***************************************

--f46d0437495533041904f85101e3-- From bogus@does.not.exist.com Mon Feb 24 10:28:22 2014 From: bogus@does.not.exist.com () Date: Mon, 24 Feb 2014 09:28:22 -0000 Subject: No subject Message-ID: community. This seems more like an abinit than xcrysden issue, hence I guess it is more likely that you will get some useful hint from the abinit mailing list. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bogus@does.not.exist.com Mon Feb 24 10:28:22 2014 From: bogus@does.not.exist.com () Date: Mon, 24 Feb 2014 09:28:22 -0000 Subject: No subject Message-ID: ab2xsf file.in (and not: ab2xsf < file.in). Further info obtainable from the source code is that the author of ab2xsf is the Gian-Marco Rignanese from the abinit group, hence if the problem persists, perhaps consider contacting him. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bogus@does.not.exist.com Mon Feb 24 10:28:22 2014 From: bogus@does.not.exist.com () Date: Mon, 24 Feb 2014 09:28:22 -0000 Subject: No subject Message-ID: When I create an input file for PWSCF and view it in XCrysDen, it only shows two atoms (attached as figure1xsf.png), whereas if I create the structure file using Materials Studio or VESTA, I see 6 atoms (attached as figure2vesta.jpeg). Is my structure correct or am I not understanding the symmetry correctly or is there a problem with XCrysDen. The relevant part of the PWSCF input file: &SYSTEM ibrav = 9, celldm(1) = 5.392713591, celldm(2) = 2.0568034482, celldm(3) = 1.736272208, nat = 1, ntyp = 1, ecutwfc = 35, ecutrho = 280, occupations = 'smearing', smearing = 'mp', degauss = 0.02, / &ELECTRONS conv_thr = 1.D-7, mixing_beta = 0.7D0, / &IONS / ATOMIC_SPECIES U 1.00 U.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS {crystal} U 0.000 0.10239 0.25 K_POINTS {automatic} 1 1 1 0 0 0 Sorry if this is trivial but I could not get it correctly no matter what all options I tried. Regards --047d7b41ce1207ccbe04fc20bc30 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear XCrysDen User= s,

I am trying to run quantum espresso (QE) calculations on bulk=20 alpha-Uranium. It belongs to space group number 63 and is a base=20 centered orthorhobmic structure.
The paper by Barrett et al. Phys Rev 129, 625 (1963) has the coordina= tes and the lattice constants (see below).
From QE's input des= cription for this bravais lattice is 9 (ibrav=3D9).
When I create an input file for PWSCF and view it in XCrysDen, it only shows two atoms (attached as figure1xsf.png), whereas if I create the=20 structure file using Materials Studio or VESTA, I see 6 atoms (attached=20 as figure2vesta.jpeg).

Is my structure correct or am I not understanding the symmetry correctl= y or is there a problem with XCrysDen.

The relevant part of th= e PWSCF input file:
=C2=A0
&SYSTEM
=C2=A0 ibrav =3D 9,
=C2= =A0 celldm(1) =3D 5.392713591,
=C2=A0 celldm(2) =3D 2.0568034482,
=C2=A0 celldm(3) =3D 1.736272208,
= =C2=A0 nat =3D 1,
=C2=A0 ntyp =3D 1,
=C2=A0 ecutwfc =3D 35,
=C2=A0= ecutrho =3D 280,
=C2=A0 occupations =3D 'smearing',
=C2=A0 s= mearing =3D 'mp',
=C2=A0 degauss =3D 0.02,
/
&ELECTRONS
=C2=A0 conv_thr =3D 1.D-7,
=C2=A0 mixing_beta =3D 0.7D= 0,
/
&IONS
/
ATOMIC_SPECIES
U=C2=A0 1.00=C2=A0 U.pbe-nd-= rrkjus.UPF
ATOMIC_POSITIONS {crystal}
U=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= 0.000=C2=A0=C2=A0=C2=A0=C2=A0 0.10239=C2=A0=C2=A0=C2=A0=C2=A0 0.25
K_PO= INTS {automatic}
=C2=A01 1 1 0 0 0


Sorry if this is trivial but I cou= ld not get it correctly no matter what all options I tried.

Re= gards
--047d7b41ce1207ccbe04fc20bc30--