Re: [SIESTA-L] atom index in non collinear spin
Dear Lucas.. Thanks now it is more clear asa On Tue, Apr 7, 2009 at 3:32 PM, Lucas Fernandez Seivane wrote: > Dear Asa > > You have to explicitly say all atoms. The polarization is per-atom, > and not per-species. > regards > > Lucas > > On Tue, Apr 7, 2009 at 09:36, asa aravindh wrote: > > Dear Ricardo.. > > Thanks for your reply.. actually what I meant is ,, if all atoms are > > polarised.. > > is it enough to give only the species index or we hav to give all atoms > one > > by one explicitly...? > > regards > > asa > > > > > > On Tue, Apr 7, 2009 at 3:44 AM, Ricardo Faccio > wrote: > >> > >> Dear Asa > >> What you did is ok, you can only select the polarized atoms. > >> Regards > >> Ricardo > >> > - > >> Dr. Ricardo Faccio > >> > >> Mail: Cryssmat-Lab., Cátedra de Física, DETEMA > >> Facultad de Química, Universidad de la República > >>Av. Gral. Flores 2124, C.C. 1157 > >>C.P. 11800, Montevideo, Uruguay. > >> E-mail: rfac...@fq.edu.uy > >> Phone: 598 2 924 98 59 > >> 598 2 929 06 48 > >> Fax:598 2 9241906 > >> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > >> > >> > - > >> > >> - Original Message - > >> From: asa aravindh > >> To: SIESTA-L@listserv.uam.es > >> Sent: Monday, April 06, 2009 8:55 AM > >> Subject: [SIESTA-L] atom index in non collinear spin > >> Hi all... > >> I have a doubt regarding giving atom index in non-collinear > calculations.. > >> suppose if my system contain total 10 atoms.. . and in that 3 atom > species > >> are there, say 1,2 and 3.then while specifying spin direction in DM Init > >> spin, is it correct if I specify only for the 3 non equivalent atoms..if > all > >> atoms are having same spin orientation... > >> like , > >> %block DM.InitSpin > >> 1 + > >> 2 + > >> 3 + > >> %endblock DM.InitSpin > >> or have I need to specify for all the 10 atom numbers here from 1 to > >> 10like 1 + , 2 + ..10 + > >> can anybody please clarify my doubt?? > >> thanks in advance > >> Asa > >> > >> > > > > > > > > -- > > Assa Aravindh.S > > Research Scholar > > Theory and Computational Studies Section, > > Material Science Division, IGCAR, India > > > -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
Re: [SIESTA-L] atom index in non collinear spin
Dear Ricardo.. Thanks for your reply.. actually what I meant is ,, if all atoms are polarised.. is it enough to give only the species index or we hav to give all atoms one by one explicitly...? regards asa On Tue, Apr 7, 2009 at 3:44 AM, Ricardo Faccio wrote: > Dear Asa > What you did is ok, you can only select the polarized atoms. > Regards > Ricardo > - > Dr. Ricardo Faccio > > Mail: Cryssmat-Lab., Cátedra de Física, DETEMA > Facultad de Química, Universidad de la República >Av. Gral. Flores 2124, C.C. 1157 >C.P. 11800, Montevideo, Uruguay. > E-mail: rfac...@fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax:598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > > --------- > > - Original Message - > *From:* asa aravindh > *To:* SIESTA-L@listserv.uam.es > *Sent:* Monday, April 06, 2009 8:55 AM > *Subject:* [SIESTA-L] atom index in non collinear spin > > Hi all... > I have a doubt regarding giving atom index in non-collinear calculations.. > suppose if my system contain total 10 atoms.. . and in that 3 atom species > are there, say 1,2 and 3.then while specifying spin direction in DM Init > spin, is it correct if I specify only for the 3 non equivalent atoms..if all > atoms are having same spin orientation... > like , > %block DM.InitSpin > 1 + > 2 + > 3 + > %endblock DM.InitSpin > or have I need to specify for all the 10 atom numbers here from 1 to > 10like 1 + , 2 + ..10 + > can anybody please clarify my doubt?? > thanks in advance > Asa > > > -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
[SIESTA-L] atom index in non collinear spin
Hi all... I have a doubt regarding giving atom index in non-collinear calculations.. suppose if my system contain total 10 atoms.. . and in that 3 atom species are there, say 1,2 and 3.then while specifying spin direction in DM Init spin, is it correct if I specify only for the 3 non equivalent atoms..if all atoms are having same spin orientation... like , %block DM.InitSpin 1 + 2 + 3 + %endblock DM.InitSpin or have I need to specify for all the 10 atom numbers here from 1 to 10like 1 + , 2 + ..10 + can anybody please clarify my doubt?? thanks in advance Asa
[SIESTA-L] GGA-PBE pseudo for Mg and O
Dear siesta users, I am in need of GGA-PBE pseudo potentials for Mg and O. I could only find the LDA flavours in the siesta pseudo base. I will be grateful if anybody can share with me the GGA pseudopotentials and basis for Mg and O. Thanks in advance, Asa -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
Re: [SIESTA-L] problem in FERMID
Dear all.. Thanks for all your suggestions. I have posted the querry to the smeagol mailing list. Best regards, Asa On Wed, Feb 11, 2009 at 2:25 PM, Stefano Sanvito wrote: > Dear Asa, > > Pablo is right, this sounds more like a Smeagol problem ... in particular > if the problem does not happen with Siesta (note however that Smeagol runs > on Siesta 1.3). Please re-post your message, with details which will allow > us to understand, at: > > smeagol-disc...@lists.tchpc.tcd.ie > > Stefano > -- > > = > Prof. Stefano Sanvito, > Director of Graduate Studies School of Physics > > School of Physics,Ph. : +353-1-8963065 > Trinity College Dublin, Mob.: +353-87-9595384 > Dublin 2, IRELAND Fax.: +353-1-6711759 > > http://www.tcd.ie/Physics/People/Stefano.Sanvito/ > = > -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
Re: [SIESTA-L] problem in FERMID
Dear prof. Pablo, I rally dnt know the actual cause of the problem, but I have seen that there are discussions in the forum on same issue. For running smeagol, for the electronic structure part the siesta_1.3f1p version is used. Calculations with siesta.2.0 version is running successfully. I expect responses from people who have similar experiences. Thanks, Asa On Wed, Feb 11, 2009 at 1:03 PM, Pablo Ordejón Rontomé wrote: > > > Are you sure this is an issue of Siesta, or is it a Smeagol problem?? >This list does not support questions related to Smeagol. > > Pablo Ordejon. > > > > El 11/02/09 7:08, "asa aravindh" escribió: > > Dear all.. > I have a question regarding the running of smeagol package. When I tried to > run the examples in the smeagol.1.0b distribution, I am getting the > following error message and the program stops . > > --- > siesta: === > Begin MD step = 1 > === > > superc: Internal auxiliary supercell: 1 x 1 x 3 = 3 > superc: Number of atoms, orbitals, and projectors: 6 624 > > InitMesh: MESH =80 x80 x36 = 230400 > InitMesh: Mesh cutoff (required, used) = 100.000 114.217 Ry > > * Maximum dynamic memory allocated =16 MB > > stepf: Fermi-Dirac step function > FERMID: ITERATION HAS NOT CONVERGED. > FERMID: QTOT,SUMQ= 2.00 NaN > > --- > I have seen that this problem is being discussed in the siesta list , > still I couldnt find a solution after trying various options , like changing > the tolerance, mesh cut off.. > But I am not getting any such problems if I am runing the siesta.2.0 > version. > Any suggestion would be greatly appreaciated. > Thanks in advance > Asa > > > > > > > Prof. Pablo Ordejon > CIN2: Centre d'Investigació en Nanociència i Nanotecnologia (CSIC-ICN) > > Postal Address (temporary): > CIN2 > Edificio ETSE, Planta 2, Despacho QC-2107 > Campus de la U.A.B. > 08193 Bellaterra, Barcelona (Spain) > > Phone: +34 93 581 37 98 > Fax: +34 93 581 37 97 > Email: pablo.orde...@cin2.es > -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
[SIESTA-L] problem in FERMID
Dear all.. I have a question regarding the running of smeagol package. When I tried to run the examples in the smeagol.1.0b distribution, I am getting the following error message and the program stops . --- siesta: === Begin MD step = 1 === superc: Internal auxiliary supercell: 1 x 1 x 3 = 3 superc: Number of atoms, orbitals, and projectors: 6 624 InitMesh: MESH =80 x80 x36 = 230400 InitMesh: Mesh cutoff (required, used) = 100.000 114.217 Ry * Maximum dynamic memory allocated =16 MB stepf: Fermi-Dirac step function FERMID: ITERATION HAS NOT CONVERGED. FERMID: QTOT,SUMQ= 2.00 NaN --- I have seen that this problem is being discussed in the siesta list , still I couldnt find a solution after trying various options , like changing the tolerance, mesh cut off.. But I am not getting any such problems if I am runing the siesta.2.0 version. Any suggestion would be greatly appreaciated. Thanks in advance Asa -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
[SIESTA-L] regarding magnetic moment again
Dear Andrei Postnikov, I am really thankful to you for the valuable suggestions. 1. I have experimented by both setting the DM.InitSpin block and not. In my collinear calculations, anyhow it is not making much of a change regarding the magnetic moment values 2. I feel that eventhough the magnetic moments of 3d atoms for 2D and 1D systems are larger than the corresponding bulk, the values I am getting for Fe and Co is much higher. I have to figure out this by properly setting other input parameters. 3. As I just started learnig Siesta, I think it will take some time for me to get a feel for the numbers Siesta give. 4. I understood your point regarding the k mesh. I have to do convergence tests to find out the k grid values in periodic and non-periodic directions. I think a fine kgrid can give me more accurate magnetic moment . 5. I do have Xcrysden installed. Visualization using the Sies2xsf tool correctly gave the bcc(110) nanowire structure With best regards, Asa > -- Assa Aravindh.S Research Scholar Theory and Computational Studies Section, Material Science Division, IGCAR, India
[SIESTA-L] magnetic moment
Dear siesta users.. I am new user of siesta. I am doing calculations of an Fe/Co nanowire. My system contains 18 atoms. As both Fe and Co are magnetic, I have set the spin polarised flag true. In the output it is shown that Total spin polarization (Qup-Qdown) =5.471783 I understand that this value is in bohr magneton and it is the total magnetization of the nanowire. But this value is very low as the individual magnetic moments of Fe and Co are around 2.2 and 1.7 respectvely. Previously I have done calculations of the same system in VASP and the total magneticmoment of the system is 36 bohr magneton.. Can anybody please explain what is wrong / what is the way to get the local and total magnetic moment frm the siesta output file..I am doing a collinear calculation.. thanks in advance Asa
