[Pw_forum] QE & Xcrysden
naphtaly moro
moronaphtaly84 at gmail.com
Wed Mar 10 18:07:47 CET 2010
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
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> 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
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>
>
> --
> -----------------------------------------------------
> 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
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>
> 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
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>
> 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
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> ------------------------------
>
> 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
>
>
>
> ------------------------------
>
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