Dear Re: Ngoc Linh Nguyen, Giovanni Cantele & Sebastijan Peljhan I am working on the various phases of GaAs. at normal conditions, GaAs assumes a Zincblende structures fcc ibrav=2, as pressure increases it assumes Rocksalt structure and then assumes a CsCl structure which is bcc ibrav=3 that is why my input as i posted it. Can you advice me further? Regards
On 3/10/10, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: About supercell App. (Ngoc Linh Nguyen) > 2. QE & Xcrysden (naphtaly moro) > 3. Re: QE & Xcrysden (Ngoc Linh Nguyen) > 4. Re: QE & Xcrysden (Giovanni Cantele) > 5. Re: QE & Xcrysden (Sebastijan Peljhan) > 6. Re: calculating the cell parameters in crystals (Masoud Nahali) > 7. SURFACE RECONSTRUCTION USING RELAX CALCULATION (mohnish pandey) > 8. vc-relax with starting_magnetization (Bryan M. Wong) > 9. Re: SURFACE RECONSTRUCTION USING RELAX CALCULATION > (Ngoc Linh Nguyen) > 10. Re: SURFACE RECONSTRUCTION USING RELAX CALCULATION > (Giovanni Cantele) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Mar 2010 09:24:44 +0100 > From: Ngoc Linh Nguyen <nnlinh at sissa.it> > Subject: Re: [Pw_forum] About supercell App. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4B97574C.8000801 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > mohsen modaresi wrote: >> Hi every body >> I read all discussion about 'super cell' generation, But i can't >> understand. >> In 2009 there is a discussion about supercell generation and any body >> refferd to PHON code, But i could'nt install PHON. > PHON is used when you want to consider the more complicated structure, > but it's not the only way. >> Is there any why to determine the parameters? > You mean "Is there any ways to determine the parameters?" ? > of course, Yes. Let refer the previous question "calculation the cell > parameters in crystals" in forum. > >> for example could you explain this part of a SCF calculation for >> Pt-H2-Pt chain. >> ibrav=8, >> celldm(1)=18.0,------>This >> celldm(2)=1.0,--------->This >> celldm(3)=2.21412992, -----> This >> ... >> ATOMIC_POSITIONS {angstrom} >> Pt 0.000 0.000 0.000----->and this >> Pt 0.000 0.000 2.410----->and this >> Pt 0.000 0.000 4.820----->and this >> Pt 0.000 0.000 7.230----->and this >> H 0.000 0.000 8.900----->and this >> H 0.000 0.000 9.780----->and this >> Pt 0.000 0.000 11.450----->and this >> Pt 0.000 0.000 13.860----->and this >> Pt 0.000 0.000 16.270----->and this >> Pt 0.000 0.000 18.680----->and this >> suppose we want to change (Pt--->Cu) how can i get new parameters? > With a simple orthorhombic lattice, you need the value of lattice > constant of Cu, and estimate the celldm(1), celldm(2), and celldm(3) of > unit cell from that value. > > Let do similarly to Pt but for Cu values > > Good luck > > Linh > >> Thanks so much for your answers >> Mohsen Modarsei >> M.Sc student of solid state physics\ >> Ferdowsi University of Mashhad >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- > ----------------------------------------------------- > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, > via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > ----------------------------------------------------- > "The physics is theoretical but the fun is real" > > > > > ------------------------------ > > Message: 2 > Date: Wed, 10 Mar 2010 11:44:52 +0300 > From: naphtaly moro <moronaphtaly84 at gmail.com> > Subject: [Pw_forum] QE & Xcrysden > To: pw_forum at pwscf.org > Message-ID: > <fe3b32711003100044t31b012aen17eacad01974f4ee at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Q.E. & Xcrysden > I am working on the various phase transitions of GaAs. I am trying to > contact these structures. I ahve managed to construct the ZB and RS > structures with success. I am using Xcrysden with Quantum Espresso. > When i try to view the CsCl-GaAs structure, I only see the Ga atoms > and with no As atoms in the matrix. Can someone show me please where I > am going wrong > my input file is this > &control > prefix='GaAs', > pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo' > outdir = './tmp', > / > &system > ibrav= 3, celldm(1) =10.2, nat= 2, ntyp= 2, > ecutwfc = 12.0, > / > &electrons > / > ATOMIC_SPECIES > Ga 69.723 Ga.pbe-nsp-van.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS > Ga 0.00 0.00 0.00 > As 0.50 0.50 0.50 > K_POINTS {automatic} > 4 4 4 0 0 0 > > Thanks > > > -- > Cecil Naphtaly Moro > > > ------------------------------ > > Message: 3 > Date: Wed, 10 Mar 2010 10:07:19 +0100 > From: Ngoc Linh Nguyen <nnlinh at sissa.it> > Subject: Re: [Pw_forum] QE & Xcrysden > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4B976147.6060104 at sissa.it> > Content-Type: text/plain; charset=us-ascii; format=flowed > > naphtaly moro wrote: >> Dear Q.E. & Xcrysden >> I am working on the various phase transitions of GaAs. I am trying to >> contact these structures. I ahve managed to construct the ZB and RS >> structures with success. I am using Xcrysden with Quantum Espresso. >> When i try to view the CsCl-GaAs structure, I only see the Ga atoms >> and with no As atoms in the matrix. Can someone show me please where I >> am going wrong >> my input file is this >> &control >> prefix='GaAs', >> pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo' >> outdir = './tmp', >> / >> &system >> ibrav= 3, celldm(1) =10.2, nat= 2, ntyp= 2, >> ecutwfc = 12.0, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Ga 69.723 Ga.pbe-nsp-van.UPF >> As 74.9216 As.pbe-n-van.UPF >> ATOMIC_POSITIONS >> Ga 0.00 0.00 0.00 >> As 0.50 0.50 0.50 >> K_POINTS {automatic} >> 4 4 4 0 0 0 >> >> > You are having a wrong input structure. Namely, you chose ibrav= 3 which > means BCC lattice, so in a periodic lattice the As atoms will be > overlapped by Ga atoms. > > How to fix the problem. You should again pick up another ibrav value and > calculate the Gs and As positions. > As far as I know, GaAs lattice have a similarity to diamond lattice, so > I suggest ibrav=2, and > > Ga 0.00 0.00 0.00 > As 0.25 0.25 0.25 > > Good luck > > Linh > > >> Thanks >> >> >> > > > -- > ----------------------------------------------------- > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, > via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > ----------------------------------------------------- > "The physics is theoretical but the fun is real" > > > > > ------------------------------ > > Message: 4 > Date: Wed, 10 Mar 2010 10:12:03 +0100 > From: Giovanni Cantele <giovanni.cantele at na.infn.it> > Subject: Re: [Pw_forum] QE & Xcrysden > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <A01EC0FD-0226-4351-A0A6-040071AACB82 at na.infn.it> > Content-Type: text/plain; charset=us-ascii > > > On Mar 10, 2010, at 9:44 AM, naphtaly moro wrote: > >> Dear Q.E. & Xcrysden >> I am working on the various phase transitions of GaAs. I am trying to >> contact these structures. I ahve managed to construct the ZB and RS >> structures with success. I am using Xcrysden with Quantum Espresso. >> When i try to view the CsCl-GaAs structure, I only see the Ga atoms >> and with no As atoms in the matrix. Can someone show me please where I >> am going wrong >> my input file is this >> &control >> prefix='GaAs', >> pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo' >> outdir = './tmp', >> / >> &system >> ibrav= 3, celldm(1) =10.2, nat= 2, ntyp= 2, >> ecutwfc = 12.0, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Ga 69.723 Ga.pbe-nsp-van.UPF >> As 74.9216 As.pbe-n-van.UPF >> ATOMIC_POSITIONS >> Ga 0.00 0.00 0.00 >> As 0.50 0.50 0.50 >> K_POINTS {automatic} >> 4 4 4 0 0 0 >> >> Thanks >> >> >> -- >> Cecil Naphtaly Moro > > > The reason is that you specify ibrav = 3 that, according to what explained > in Doc/INPUT_PW.txt is a bcc lattice. > At the same time you give the ATOMIC_POSITIONS in units of the alat (namely, > a in bohr units). > Therefore, the As atom is placed at (a/2, a/2, a/2) which is, by chance (!), > also a site of the bcc lattice. > In other words, what XCrysDen sees is a Ga atom in a/2,a/2,a/2 but ALSO an > As atom at the same place and decides > to delete the latter. > Maybe you want to specify the fcc lattice (ibrav=2) and the As atom at > a/4,a/4,a/4. > > Giovanni > > > PS not very sure that ecutwfc = 12.0 whould give you converged results. > Also, because you choosed > ultrasoft pseudopotentials, you might want also check the ecutrho parameter > (by default = 4 * ecutwfc, > but larger values are needed when using US pseudo). > > -- > > Giovanni Cantele, PhD > CNR-SPIN and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 - Fax: +39 081 676346 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > http://www.nanomat.unina.it > > > > ------------------------------ > > Message: 5 > Date: Wed, 10 Mar 2010 10:22:31 +0100 > From: Sebastijan Peljhan <sebastijan.peljhan at ijs.si> > Subject: Re: [Pw_forum] QE & Xcrysden > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <1268212951.2427.22.camel at surf> > Content-Type: text/plain; charset="UTF-8" > > Dear Cecil, > > On Wed, 2010-03-10 at 11:44 +0300, naphtaly moro wrote: >> Dear Q.E. & Xcrysden >> I am working on the various phase transitions of GaAs. I am trying to >> contact these structures. I ahve managed to construct the ZB and RS >> structures with success. I am using Xcrysden with Quantum Espresso. >> When i try to view the CsCl-GaAs structure, I only see the Ga atoms >> and with no As atoms in the matrix. Can someone show me please where I >> am going wrong >> my input file is this >> &control >> prefix='GaAs', >> pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo' >> outdir = './tmp', >> / >> &system > > ibrav = 3 represents bcc cubic cell, hence the Ga and As atoms in your > structure overlap. Xcrysden actually warns you, that some of the atoms > overlap and they will be deleted. > > According to QE example06 you should try with ibrav = 2 (fcc) and As > atom at (0.25 0.25 0.25) position. > > > Cheers, > > Sebastijan > > >> ibrav= 3, celldm(1) =10.2, nat= 2, ntyp= 2, >> ecutwfc = 12.0, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Ga 69.723 Ga.pbe-nsp-van.UPF >> As 74.9216 As.pbe-n-van.UPF >> ATOMIC_POSITIONS >> Ga 0.00 0.00 0.00 >> As 0.50 0.50 0.50 >> K_POINTS {automatic} >> 4 4 4 0 0 0 >> >> Thanks >> >> > > -- > Sebastijan Peljhan > Department of Physical and Organic Chemistry > "Jozef Stefan" Institute > Jamova 39 > 1000 Ljubljana > Slovenia > > tel.:+386 1 4773 523 > fax.:+386 1 4773 822 > email: sebastijan.peljhan at IJS.SI > > > > ------------------------------ > > Message: 6 > Date: Wed, 10 Mar 2010 09:29:15 +0000 > From: Masoud Nahali <masoudnahali at live.com> > Subject: Re: [Pw_forum] calculating the cell parameters in crystals > To: Quantum Espresso <pw_forum at pwscf.org> > Message-ID: <COL114-W57423189F36CD2A9DAB553A1330 at phx.gbl> > Content-Type: text/plain; charset="windows-1256" > > > Dear Elie > > Try the VESTA software ! I am not that this can solve your problem; anyhow > is a good graphical software for solids. > > Best Wishes > Masoud Nahali > Sharif University of Technology > > > _________________________________________________________________ > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > https://signup.live.com/signup.aspx?id=60969 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100310/fcdf6482/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Wed, 10 Mar 2010 15:05:26 +0530 > From: mohnish pandey <mohnish.iitk at gmail.com> > Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <c40d64601003100135sc393a66h1f2a5ada30fac6cc at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > I want to get the results for surface reconstructions > computationally, but the problem is as we have specify the "ibrav" i.e > symmetry of the system the relax calculation only optimizes the structure > within the given symmetry. Can anybody suggest a way to model > reconstructions . > Thanks in advance, > MOHNISH > > -- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR > 09235721300 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100310/bebf5db9/attachment-0001.htm > > ------------------------------ > > Message: 8 > Date: Wed, 10 Mar 2010 01:41:29 -0800 > From: "Bryan M. Wong" <usagi at alumni.rice.edu> > Subject: [Pw_forum] vc-relax with starting_magnetization > To: pw_forum at pwscf.org > Message-ID: > <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Does anyone know how to do a "vc-relax" with the > "starting_magnetization" option turned on? > > I can always do a regular "relax" with the starting_magnetization > guess, and the structure will relax constrained to my fixed unit cell > dimensions. However, when I do a vc-relax with starting_magnetization set to > any value, the 2nd step in the cell relaxation always reverts to the > spin-unpolarized case (and the optimization will continue with the > spin-unpolarized case). > > Bryan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100310/2ea55ede/attachment-0001.htm > > ------------------------------ > > Message: 9 > Date: Wed, 10 Mar 2010 10:59:32 +0100 > From: Ngoc Linh Nguyen <nnlinh at sissa.it> > Subject: Re: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4B976D84.8070607 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > mohnish pandey wrote: >> I want to get the results for surface >> reconstructions computationally, but the problem is as we have specify >> the "ibrav" i.e symmetry of the system the relax calculation only >> optimizes the structure within the given symmetry. > Not exactly, the relax calculation plays a role to find out an optimal > configuration from an initial configuration. > If you want to consider the surface reconstruction of given material, > you should build a supercell in that the defect or adatom can be existed. > > And how to form a supercell. Let see the previous archives of PW_forum > > Good luck > > Linh > > > > > -- > ----------------------------------------------------- > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, > via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > ----------------------------------------------------- > "The physics is theoretical but the fun is real" > > > > > ------------------------------ > > Message: 10 > Date: Wed, 10 Mar 2010 11:10:20 +0100 > From: Giovanni Cantele <giovanni.cantele at na.infn.it> > Subject: Re: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <C1F70D93-3106-46A2-8DD4-A048B2C7052F at na.infn.it> > Content-Type: text/plain; charset=us-ascii > > > On Mar 10, 2010, at 10:35 AM, mohnish pandey wrote: > >> Dear users, >> I want to get the results for surface reconstructions >> computationally, but the problem is as we have specify the "ibrav" i.e >> symmetry of the system the relax calculation only optimizes the structure >> within the given symmetry. Can anybody suggest a way to model >> reconstructions . >> Thanks in advance, >> MOHNISH >> >> -- >> Mohnish Pandey >> Y6927262,4th Year dual degree student, >> Department of Chemical Engineering, >> IIT KANPUR >> 09235721300 >> > > Well, I think that a "very general" answer is difficult to give (maybe > someone more expert could try). What one usually does in studying surfaces, > is try to identify, > step by step, possible reconstructions and look at the lower energy ones. > > In practice, for a given surface direction (e.g. the silicon 100 surface) > you first identify the "minimal" unit cell (size and symmetry) in the plane > parallel to the surface. Then, you must decide > the number of atomic planes that you want to include in your calculation > (this will fix the lattice constant in the direction orthogonal to the > surface). This > will represent a so-called 1x1 model, meaning that your "surface unit cell" > is made by just one unit cell. Possible reconstruction (which means atomic > rearrangement of the atoms with respect to the ideal positions) will be, of > course, the same in all surface unit cells. > > More complicated reconstructions might arise because: > > i) there can be a surface atomic displacement different in neighbor unit > cells (for example, in the case of the cited Si surface two Si atoms in > different 1x1 cells approach to each other to form a dimer, this gives you a > 2x1 reconstruction; then two neighbor dimers can show different tilt with > respect to the surface plane, this gives a 2x2 reconstruction, etc.); to > include > this effect in your calculation you replicate your surface unit cell > (building a "supercell") in one or both directions parallel to the surface, > so as to build 1x2, 2x1, 2x2, 1x4, etc. models. Of course one should > be driven by either already known results, experimental evidences, etc. or > by physically/chemically meaningful guesses. In this case one should also be > careful to break possible symmetries that would prevent from reaching the > energy minimum. Again, in the case of the Si(100) surface, if you just > replicate the 1x1 unit cell along one surface direction, to build the 2x1 > model, the code will just give you > a structure identical to the 1x1 model, with an energy 2 times larger; so, > what you do is to move (even by a small amount) the atoms you expect will > move, namely, the two Si atoms which dimerize. Alternatively, you can > randomize the position of some/all atoms, just to break the symmetry. > > ii) there can be a reconstruction where there are more/less atoms than you > would expect in the "ideal" surface, a typical example is the case of O > vacancies in oxide surfaces. > > Because the plane-wave calculation, as you probably already know, is by > construction periodic in all directions, you must be sure to include, along > the direction orthogonal to the surface a > "vacuum space" (that means to increase the corresponding lattice parameter) > to prevent two consecutive slabs from interacting. Convergence must be > checked against the vacuum space. > Also, if you want to retrieve the "bulk surface" properties, the thickness > of your slab should be larger enough (this is controlled by the number of > atomic planes included in the unit cell) to prevent > opposite sides of a given slab from interacting with each other. > > Another issue is that the "optimal" surface unit cell might show a > completely different "symmetry" than the bulk one. For example, in the case > of Au/Pt/etc. (111) surfaces, the bulk crystal is a cubic > fcc lattice, whereas the minimal surface unit cell can be represented using > an hexagonal lattice. > > Hope this helps, > > Giovanni > > > -- > > Giovanni Cantele, PhD > CNR-SPIN and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 - Fax: +39 081 676346 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > http://www.nanomat.unina.it > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 33, Issue 37 > **************************************** > -- Cecil Naphtaly Moro
