From nicola.marzari at epfl.ch Wed Jul 1 12:37:09 2015 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Wed, 01 Jul 2015 18:37:09 +0800 Subject: [Wannier] Dissimilar results in band structures for a system obtained from Wannier90 In-Reply-To: References: <5566CD33.2070206@epfl.ch> <557E846C.4050804@epfl.ch> <557EC253.20404@epfl.ch> <558C53BE.6030609@epfl.ch> Message-ID: <5593C2D5.1050606@epfl.ch> On 29/06/2015 15:38, Seyed Mojtaba Rezaei Sani wrote: > Dear Nicola, > > Thanks. Phosphorene has four P atoms in its unit cell so considering 10 > valence bands and therefore 10 WFs, we can't fit a projection of s > orbital on every atom and bond to this number. Dear Seyed, why not? 3 bonds for every atom = 12 bonds for every unit cell, shared by two atoms = 6 WFs with s projections mid-bond 4 atoms = 4 WFs with s projections on each atom Total, 10 projections. nicola ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL Director, National Centre for Competence in Research NCCR MARVEL, EPFL From elio-physics at live.com Thu Jul 2 00:48:45 2015 From: elio-physics at live.com (Elio Physics) Date: Thu, 2 Jul 2015 01:48:45 +0300 Subject: [Wannier] wannier MoS2 bands again Message-ID: Dear all, I have been trying for quite some time now to reproduce electronic bands of a monolayer of MoS2 bands, but in vain. The bands I am getting are kind of "wiggly". Anyone can help me on this matter. the bands ' figure is attached and the .WIN input file is: num_wann = 11 num_iter=300! SYSTEMexclude_bands:1,2search_shells=20 begin unit_cell_cartbohr6.0756016508 0.0003917262 0.0000000000-3.0374615776 5.2613166712 0.00000000000.0000000000 0.0000000000 57.9146940176end unit_cell_cart begin atoms_fracMo 0.232815941 0.667313843 0.249637447S 0.756568434 0.364728921 -0.264806724S 0.756568571 0.364729538 0.764066183end atoms_frac begin ProjectionsMo:dS:pend Projections begin kpoint_pathG 0.000000 0.000000 0.000000 M 0.3333333 0.3333333 0.0000000M 0.3333333 0.3333333 0.0000000 K 0.5000000 0.0000000 0.0000000K 0.5000000 0.0000000 0.0000000 G 0.0000000 0.0000000 0.000000end kpoint_path ! KPOINTS mp_grid : 7 7 7begin kpoints 0.00000000 0.00000000 0.00000000 2.915452e-03 0.00000000 0.00000000 0.14285714 2.915452e-03 0.00000000 0.00000000 0.28571429 2.915452e-03 0.00000000 0.00000000 0.42857143 2.915452e-03 0.00000000 0.00000000 0.57142857 2.915452e-03 0.00000000 0.00000000 0.71428571 2.915452e-03 0.00000000 0.00000000 0.85714286 2.915452e-03 0.00000000 0.14285714 0.00000000 2.915452e-03 0.00000000 0.14285714 0.14285714 2.915452e-03........etc. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MoS2-WAN.eps Type: application/postscript Size: 34487 bytes Desc: not available URL: From szaboa at iis.ee.ethz.ch Thu Jul 2 11:06:17 2015 From: szaboa at iis.ee.ethz.ch (Aron Szabo) Date: Thu, 02 Jul 2015 11:06:17 +0200 Subject: [Wannier] wannier MoS2 bands again In-Reply-To: References: Message-ID: <5594FF09.6060205@iis.ee.ethz.ch> On 07/02/2015 12:48 AM, Elio Physics wrote: > Dear all, > > I have been trying for quite some time now to reproduce electronic > bands of a monolayer of MoS2 bands, but in vain. The bands I am > getting are kind of "wiggly". Anyone can help me on this matter. the > bands ' figure is attached and the .WIN input file is: > > num_wann = 11 > num_iter=300 > ! SYSTEM > exclude_bands:1,2 > search_shells=20 > > begin unit_cell_cart > bohr > 6.0756016508 0.0003917262 0.0000000000 > -3.0374615776 5.2613166712 0.0000000000 > 0.0000000000 0.0000000000 57.9146940176 > end unit_cell_cart > > begin atoms_frac > Mo 0.232815941 0.667313843 0.249637447 > S 0.756568434 0.364728921 -0.264806724 > S 0.756568571 0.364729538 0.764066183 > end atoms_frac > > begin Projections > Mo:d > S:p > end Projections > > > begin kpoint_path > G 0.000000 0.000000 0.000000 M 0.3333333 0.3333333 0.0000000 > M 0.3333333 0.3333333 0.0000000 K 0.5000000 0.0000000 0.0000000 > K 0.5000000 0.0000000 0.0000000 G 0.0000000 0.0000000 0.000000 > end kpoint_path > > > ! KPOINTS > > mp_grid : 7 7 7 > begin kpoints > 0.00000000 0.00000000 0.00000000 2.915452e-03 > 0.00000000 0.00000000 0.14285714 2.915452e-03 > 0.00000000 0.00000000 0.28571429 2.915452e-03 > 0.00000000 0.00000000 0.42857143 2.915452e-03 > 0.00000000 0.00000000 0.57142857 2.915452e-03 > 0.00000000 0.00000000 0.71428571 2.915452e-03 > 0.00000000 0.00000000 0.85714286 2.915452e-03 > 0.00000000 0.14285714 0.00000000 2.915452e-03 > 0.00000000 0.14285714 0.14285714 2.915452e-03 > . > . > .. > ....etc. > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier You should use a denser k point grid in the x-y plane, but you don't need more than one point in the z direction, since the third lattice vector is quite large. Try a 15x15x1 MP grid (both in the scf calculation and in Wannier90). Make sure that the electronic calculation converged correctly, and do a band structure calculation with pw.x, to see whether these wiggly bands are the results of Wannier90 or the DFT calculation. And are you using exactly 13 bands? If not, then you should also exclude those bands above 13. And check for the convergence of the Wannier functions' spreads. Normally it should be around 2-3 Angstrom per function even in the first step, and it should decrease quickly below 2 A with these projections. But I think this error is probably the result of a non-converged scf simulation. You could also try to increase the number of bands in the scf simulation, because depending on the algorithm the highest bands might be inaccurate. Then just exclude those bands in the .win file. Best, Aron -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.gibertini at epfl.ch Thu Jul 2 13:21:07 2015 From: marco.gibertini at epfl.ch (Gibertini Marco) Date: Thu, 02 Jul 2015 13:21:07 +0200 Subject: [Wannier] wannier MoS2 bands again In-Reply-To: References: Message-ID: <55951EA3.20309@epfl.ch> Dear Elio, it seems to me that your atomic coordinates make no sense. There are 15 Ang of vacuum between the plane of Mo and S atoms!! In addition, the inplane coordinates do not respect the symmetry of the system. As Aron Szabo suggested already some time ago, it is not needed to sample the vertical direction with 7 k-points if your are studying a monolayer. More in-plane k-points might be needed instead. Hope this helps! Kind regards, Marco Gibertini On 07/02/2015 12:48 AM, Elio Physics wrote: > Dear all, > > I have been trying for quite some time now to reproduce electronic > bands of a monolayer of MoS2 bands, but in vain. The bands I am > getting are kind of "wiggly". Anyone can help me on this matter. the > bands ' figure is attached and the .WIN input file is: > > num_wann = 11 > num_iter=300 > ! SYSTEM > exclude_bands:1,2 > search_shells=20 > > begin unit_cell_cart > bohr > 6.0756016508 0.0003917262 0.0000000000 > -3.0374615776 5.2613166712 0.0000000000 > 0.0000000000 0.0000000000 57.9146940176 > end unit_cell_cart > > begin atoms_frac > Mo 0.232815941 0.667313843 0.249637447 > S 0.756568434 0.364728921 -0.264806724 > S 0.756568571 0.364729538 0.764066183 > end atoms_frac > > begin Projections > Mo:d > S:p > end Projections > > > begin kpoint_path > G 0.000000 0.000000 0.000000 M 0.3333333 0.3333333 0.0000000 > M 0.3333333 0.3333333 0.0000000 K 0.5000000 0.0000000 0.0000000 > K 0.5000000 0.0000000 0.0000000 G 0.0000000 0.0000000 0.000000 > end kpoint_path > > > ! KPOINTS > > mp_grid : 7 7 7 > begin kpoints > 0.00000000 0.00000000 0.00000000 2.915452e-03 > 0.00000000 0.00000000 0.14285714 2.915452e-03 > 0.00000000 0.00000000 0.28571429 2.915452e-03 > 0.00000000 0.00000000 0.42857143 2.915452e-03 > 0.00000000 0.00000000 0.57142857 2.915452e-03 > 0.00000000 0.00000000 0.71428571 2.915452e-03 > 0.00000000 0.00000000 0.85714286 2.915452e-03 > 0.00000000 0.14285714 0.00000000 2.915452e-03 > 0.00000000 0.14285714 0.14285714 2.915452e-03 > . > . > .. > ....etc. > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- **** Marco Gibertini **************************************** Post-doctoral Research Scientist Theory and Simulation of Materials ?cole Polytechnique F?d?rale de Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.m.rezaeisani at gmail.com Fri Jul 3 12:48:03 2015 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Fri, 3 Jul 2015 15:18:03 +0430 Subject: [Wannier] Dissimilar results in band structures for a system obtained from Wannier90 In-Reply-To: <5593C2D5.1050606@epfl.ch> References: <5566CD33.2070206@epfl.ch> <557E846C.4050804@epfl.ch> <557EC253.20404@epfl.ch> <558C53BE.6030609@epfl.ch> <5593C2D5.1050606@epfl.ch> Message-ID: Dear Nicola, Thank you very much. I changed projection to s orbital as you suggested. Very good band structure is obtained. The imaginary part of Hamiltonian had a great decrease from 0.189159 to 0.000098 although there is no significant change in spread (~ 60 Bohr^2). The problem is that we are still stick to the previous error: *---------------------------------------------------------------------------* | TRANSPORT | *---------------------------------------------------------------------------* Calculation of Quantum Conductance and DoS: bulk mode Maximum imaginary part of the real-space Hamiltonian: 0.189159 ------------------------------------------------------------------------------ Maximum real part of the real-space Hamiltonian at each lattice point -------------------------------------------------------------- Lattice point R Max |H_ij(R)| -1 0.000000 0 7.773991 1 0.000000 -------------------------------------------------------------- Number of unit cells inside the principal layer: 0 Number of Wannier Functions inside the principal layer: 0 Calculating quantum conductance and density of states... ERROR: IN ZGESV IN tran_transfer, INFO= -4 Exiting....... tran_transfer: problem in ZGESV 1 Would you please help me with this? On Wed, Jul 1, 2015 at 3:07 PM, Nicola Marzari wrote: > > > On 29/06/2015 15:38, Seyed Mojtaba Rezaei Sani wrote: > >> Dear Nicola, >> >> Thanks. Phosphorene has four P atoms in its unit cell so considering 10 >> valence bands and therefore 10 WFs, we can't fit a projection of s >> orbital on every atom and bond to this number. >> > > > Dear Seyed, > > > why not? > > 3 bonds for every atom = 12 bonds for every unit cell, shared by two > atoms = 6 WFs with s projections mid-bond > > 4 atoms = 4 WFs with s projections on each atom > > Total, 10 projections. > > nicola > > > > > > ---------------------------------------------------------------------- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > Director, National Centre for Competence in Research NCCR MARVEL, EPFL > -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.m.rezaeisani at gmail.com Tue Jul 7 07:59:38 2015 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Tue, 7 Jul 2015 10:29:38 +0430 Subject: [Wannier] Dissimilar results in band structures for a system obtained from Wannier90 In-Reply-To: References: <5566CD33.2070206@epfl.ch> <557E846C.4050804@epfl.ch> <557EC253.20404@epfl.ch> <558C53BE.6030609@epfl.ch> <5593C2D5.1050606@epfl.ch> Message-ID: Dear Nicola, Any help on this? On Fri, Jul 3, 2015 at 3:18 PM, Seyed Mojtaba Rezaei Sani < s.m.rezaeisani at gmail.com> wrote: > Dear Nicola, > > Thank you very much. I changed projection to s orbital as you suggested. > Very good band structure is obtained. > The imaginary part of Hamiltonian had a great decrease from 0.189159 to > 0.000098 although > there is no significant change in spread (~ 60 Bohr^2). The problem is > that we are still stick to the previous error: > > > *---------------------------------------------------------------------------* > | > TRANSPORT | > > *---------------------------------------------------------------------------* > > > Calculation of Quantum Conductance and DoS: bulk mode > > Maximum imaginary part of the real-space Hamiltonian: 0.189159 > > > ------------------------------------------------------------------------------ > Maximum real part of the real-space Hamiltonian at each lattice point > -------------------------------------------------------------- > Lattice point R Max |H_ij(R)| > -1 0.000000 > 0 7.773991 > 1 0.000000 > -------------------------------------------------------------- > > Number of unit cells inside the principal layer: 0 > Number of Wannier Functions inside the principal layer: 0 > > Calculating quantum conductance and density of states... > ERROR: IN ZGESV IN tran_transfer, INFO= -4 > Exiting....... > tran_transfer: problem in ZGESV 1 > > Would you please help me with this? > > On Wed, Jul 1, 2015 at 3:07 PM, Nicola Marzari > wrote: > >> >> >> On 29/06/2015 15:38, Seyed Mojtaba Rezaei Sani wrote: >> >>> Dear Nicola, >>> >>> Thanks. Phosphorene has four P atoms in its unit cell so considering 10 >>> valence bands and therefore 10 WFs, we can't fit a projection of s >>> orbital on every atom and bond to this number. >>> >> >> >> Dear Seyed, >> >> >> why not? >> >> 3 bonds for every atom = 12 bonds for every unit cell, shared by two >> atoms = 6 WFs with s projections mid-bond >> >> 4 atoms = 4 WFs with s projections on each atom >> >> Total, 10 projections. >> >> nicola >> >> >> >> >> >> ---------------------------------------------------------------------- >> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL >> Director, National Centre for Competence in Research NCCR MARVEL, EPFL >> > > > > -- > Seyed Mojtaba Rezaei Sani > > Institute for Research in Fundamental Sciences (IPM) > School of Nano-Science > Shahid Farbin Alley > Shahid Lavasani st > P.O. Box 19395-5531 > Tehran, Iran > Tel: +98 21 2310 (3069) > -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -------------- next part -------------- An HTML attachment was scrubbed... URL: From zaldolam at email.uark.edu Tue Jul 7 09:45:13 2015 From: zaldolam at email.uark.edu (Zeina Al-Dolami) Date: Tue, 7 Jul 2015 02:45:13 -0500 Subject: [Wannier] initial projections Message-ID: Dear wannier90's owners and developers, I have been trying to understand the examples well before going further. One of the relevant topic that I am having hard time understanding is the initial projections and the best way to define them for a system. I have read the user guide and tutorials to gain more insight. Also, I have found nice details and explanations related to the projections of carbon nano tubes and graphene systems based on the examples provided within wannier90. However, I am totally confused about the way that these projections are found. My questions might be related to the chemistry, but I need your help to start and then go from there. My questions are: 1. Prof.Nicola has mentioned that s-like projections are in the middle of each bond that has to be identified correctly. How to identify them? To clarify, example13 has this projection c= -2.7274, -1.9677, -0.6157 :s . How to find these numbers for the center of projections? Is there mathematical formula or chemistry reasons? How are they found preciously for any system? 2. One of the pz projections of the same example is c= 3.3780, -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1. The center of CNT is 0,0,0. In the forum, there is an emphasis that the direction of the CNT along z-axis, so z and x are identified to be along z direction. In case CNT is along x, should we have z=0.0,-0.7128, -0.6157 :x=1,0,0 or I am confused by the statement in the forum?? 3.In example15, one of the pz projections is c=1.58342228,1.15042363,0.0:pz:z=0.809016993454,0.587785253559,0.0:x=0,0,1 How to get these numbers z=0.809016993454,0.587785253559,0.0? Is it same way as question 1? 4. How or why do we choose a specific number of projections? I am assuming it depends on the MLWF and bands that we are interested in but not sure. You can tell from my questions that I am totally confused. Any feedback and comments from anyone are greatly appreciated. Apologies for such long email and questions. Looking forward to hearing from you. Many thanks in advance -- Zeina Al-Dolami PhD Candidate Microelectronics and Photonics Graduate Program University of Arkansas Fayetteville, AR 72701 Office: PHYS 244 Email: zaldolam at email.uark.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovanni.cantele at spin.cnr.it Tue Jul 7 11:13:35 2015 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Tue, 7 Jul 2015 11:13:35 +0200 Subject: [Wannier] initial projections In-Reply-To: References: Message-ID: <7A8D000A-1B63-46CF-8971-BA5D2ED4139D@spin.cnr.it> > On 07 Jul 2015, at 09:45, Zeina Al-Dolami wrote: > > Dear wannier90's owners and developers, > I have been trying to understand the examples well before going further. One of the relevant topic that I am having hard time understanding is the initial projections and the best way to define them for a system. I have read the user guide and tutorials to gain more insight. Also, I have found nice details and explanations related to the projections of carbon nano tubes and graphene systems based on the examples provided within wannier90. However, I am totally confused about the way that these projections are found. My questions might be related to the chemistry, but I need your help to start and then go from there. My questions are: > > 1. Prof.Nicola has mentioned that s-like projections are in the middle of each bond that has to be identified correctly. How to identify them? To clarify, example13 has this projection c= -2.7274, -1.9677, -0.6157 :s . How to find these numbers for the center of projections? Is there mathematical formula or chemistry reasons? How are they found preciously for any system? This example refers to a carbon nanotube, where the initial guess consists in one pz orbital (with the z axis properly oriented) per each C atom, and one s orbital at each bond. This reflects the chemistry of C-based nanostructures (C nanotubes, graphene), where the sp2 hybridisation occurs. The numbers you mention are the coordinates of the middle point between the atoms C -3.151822438 -1.395018907 -0.615700000 C -2.303060204 -2.540325691 -0.615700000 that are given in input. You find an s orbital at each middle bond. > > 2. One of the pz projections of the same example is c= 3.3780, -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1. The center of CNT is 0,0,0. > In the forum, there is an emphasis that the direction of the CNT along z-axis, so z and x are identified to be along z direction. In case CNT is along x, should we have z=0.0,-0.7128, -0.6157 :x=1,0,0 or I am confused by the statement in the forum?? The carbon nanotube axis, of the mentioned example, is parallel to the z axis. However, for each C atom, the corresponding pz orbital is not parallel to the z axis but orthogonal to the nanotube surface, as the chemistry of a C nanotube tells you. In other words, for each C atom, you must calculate the direction normal to the nanotube and tell wannier90 to use as an initial guess a pz orbital along that direction. Should you have graphene, this problem would not occur, in that case all pz orbital would be parallel to each other. > > 3.In example15, one of the pz projections is c=18,1.15042363,0.0:pz:z=0.809016993454,0.587785253559,0.0:x=0,0,1 > How to get these numbers z=0.809016993454,0.587785253559,0.0? Is it same way as question 1? In this case, at variance with question 1, you are looking for a pz guess. The center is on the 1st carbon atom C 1.58342228 1.15042363 0.00000000 so the coordinates that follow ?c=? are the same as those of this C atom. What follows, as specified before, is the direction of the axis along with to put the pz orbital. These are obtained (more difficult to say than to do it!) by: i) identifying the three first neighbours (manually, for example visualizing the structure with XCrysDen or automatically, by writing some simple script once you understand the algorithm) of the C atom , say P1, P2, P3 ii) compute M1 = (P1 - P2)/Norm[P1 - P2] and M2 = (P1 - P3)/Norm[P1 - P3], these are the versors connecting P1 and P2 and P1 and P3, respectively iii) compute V = (M2 x M3)/Norm[(M2 x M3)], where x = cross product (V is normal to both M2 and M3) iv) because the ideal nanotube surface is such that at each point the normal is always perpendicular to the nanotube axis, get rid of the V component parallel to the nanotube axis, so V? = V - (V . z) z, where . = dot product and z is the versor of the nanotube axis The result is 0.809017, 0.587785, 0., that should answer your question > > 4. How or why do we choose a specific number of projections? I am assuming it depends on the MLWF and bands that we are interested in but not sure. Yes it depends, generally you should recognise the chemistry of your system and the character (in terms of atomic orbitals or their combinations) of the bands you are interested in (you might what to reproduce only a subset of your band structure, for example group of bands close to the Fermi level). > > You can tell from my questions that I am totally confused. Any feedback and comments from anyone are greatly appreciated. Apologies for such long email and questions. Looking forward to hearing from you. Many thanks in advance Actually, apart from simple systems, choosing the proper initial guess might be a quite hard task. Giovanni > > -- > Zeina Al-Dolami > PhD Candidate > Microelectronics and Photonics Graduate Program > University of Arkansas > Fayetteville, AR 72701 > Office: PHYS 244 > Email: zaldolam at email.uark.edu _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.mostofi at imperial.ac.uk Tue Jul 7 22:55:49 2015 From: a.mostofi at imperial.ac.uk (Mostofi, Arash) Date: Tue, 7 Jul 2015 20:55:49 +0000 Subject: [Wannier] Dissimilar results in band structures for a system obtained from Wannier90 In-Reply-To: References: <5566CD33.2070206@epfl.ch> <557E846C.4050804@epfl.ch> <557EC253.20404@epfl.ch> <558C53BE.6030609@epfl.ch> <5593C2D5.1050606@epfl.ch> Message-ID: Dear Seyed, The transport code currently only works for quasi-one-dimensional systems, i.e., systems that are isolated in both directions perpendicular to the transport direction. Examples include nanowires, nanotubes, nanoribbons etc. If I?ve understood your emails correctly, you are considering a planar system with periodicity in the x and y directions. Best wishes, Arash ? Dr Arash Mostofi ? www.mostofigroup.org Reader in Theory and Simulation of Materials Imperial College London Director, Thomas Young Centre @Imperial Warden, Wilkinson & Weeks Hall On 7 Jul 2015, at 06:59, Seyed Mojtaba Rezaei Sani > wrote: Dear Nicola, Any help on this? On Fri, Jul 3, 2015 at 3:18 PM, Seyed Mojtaba Rezaei Sani > wrote: Dear Nicola, Thank you very much. I changed projection to s orbital as you suggested. Very good band structure is obtained. The imaginary part of Hamiltonian had a great decrease from 0.189159 to 0.000098 although there is no significant change in spread (~ 60 Bohr^2). The problem is that we are still stick to the previous error: *---------------------------------------------------------------------------* | TRANSPORT | *---------------------------------------------------------------------------* Calculation of Quantum Conductance and DoS: bulk mode Maximum imaginary part of the real-space Hamiltonian: 0.189159 ------------------------------------------------------------------------------ Maximum real part of the real-space Hamiltonian at each lattice point -------------------------------------------------------------- Lattice point R Max |H_ij(R)| -1 0.000000 0 7.773991 1 0.000000 -------------------------------------------------------------- Number of unit cells inside the principal layer: 0 Number of Wannier Functions inside the principal layer: 0 Calculating quantum conductance and density of states... ERROR: IN ZGESV IN tran_transfer, INFO= -4 Exiting....... tran_transfer: problem in ZGESV 1 Would you please help me with this? On Wed, Jul 1, 2015 at 3:07 PM, Nicola Marzari > wrote: On 29/06/2015 15:38, Seyed Mojtaba Rezaei Sani wrote: Dear Nicola, Thanks. Phosphorene has four P atoms in its unit cell so considering 10 valence bands and therefore 10 WFs, we can't fit a projection of s orbital on every atom and bond to this number. Dear Seyed, why not? 3 bonds for every atom = 12 bonds for every unit cell, shared by two atoms = 6 WFs with s projections mid-bond 4 atoms = 4 WFs with s projections on each atom Total, 10 projections. nicola ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL Director, National Centre for Competence in Research NCCR MARVEL, EPFL -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: From zaldolam at email.uark.edu Wed Jul 8 20:55:00 2015 From: zaldolam at email.uark.edu (Zeina Al-Dolami) Date: Wed, 8 Jul 2015 13:55:00 -0500 Subject: [Wannier] initial projections In-Reply-To: <7A8D000A-1B63-46CF-8971-BA5D2ED4139D@spin.cnr.it> References: <7A8D000A-1B63-46CF-8971-BA5D2ED4139D@spin.cnr.it> Message-ID: <-3652220572908964699@unknownmsgid> Dr. Giovanni, Thanks so much for your nice explanation. I just want to make sure of your answer to question 3. Did you mean M1 and M2 in answer 3 step 3?? What is M3? Thanks again and looking forward to hearing from you Zeina On Jul 7, 2015, at 4:13 AM, Giovanni Cantele wrote: On 07 Jul 2015, at 09:45, Zeina Al-Dolami wrote: Dear wannier90's owners and developers, I have been trying to understand the examples well before going further. One of the relevant topic that I am having hard time understanding is the initial projections and the best way to define them for a system. I have read the user guide and tutorials to gain more insight. Also, I have found nice details and explanations related to the projections of carbon nano tubes and graphene systems based on the examples provided within wannier90. However, I am totally confused about the way that these projections are found. My questions might be related to the chemistry, but I need your help to start and then go from there. My questions are: 1. Prof.Nicola has mentioned that s-like projections are in the middle of each bond that has to be identified correctly. How to identify them? To clarify, example13 has this projection c= -2.7274, -1.9677, -0.6157 :s . How to find these numbers for the center of projections? Is there mathematical formula or chemistry reasons? How are they found preciously for any system? This example refers to a carbon nanotube, where the initial guess consists in one pz orbital (with the z axis properly oriented) per each C atom, and one s orbital at each bond. This reflects the chemistry of C-based nanostructures (C nanotubes, graphene), where the sp2 hybridisation occurs. The numbers you mention are the coordinates of the middle point between the atoms C -3.151822438 -1.395018907 -0.615700000 C -2.303060204 -2.540325691 -0.615700000 that are given in input. You find an s orbital at each middle bond. 2. One of the pz projections of the same example is c= 3.3780, -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1. The center of CNT is 0,0,0. In the forum, there is an emphasis that the direction of the CNT along z-axis, so z and x are identified to be along z direction. In case CNT is along x, should we have z=0.0,-0.7128, -0.6157 :x=1,0,0 or I am confused by the statement in the forum?? The carbon nanotube axis, of the mentioned example, is parallel to the z axis. However, for each C atom, the corresponding pz orbital is not parallel to the z axis but orthogonal to the nanotube surface, as the chemistry of a C nanotube tells you. In other words, for each C atom, you must calculate the direction normal to the nanotube and tell wannier90 to use as an initial guess a pz orbital along that direction. Should you have graphene, this problem would not occur, in that case all pz orbital would be parallel to each other. 3.In example15, one of the pz projections is c=18,1.15042363,0.0:pz:z=0.809016993454,0.587785253559,0.0:x=0,0,1 How to get these numbers z=0.809016993454,0.587785253559,0.0? Is it same way as question 1? In this case, at variance with question 1, you are looking for a pz guess. The center is on the 1st carbon atom C 1.58342228 1.15042363 0.00000000 so the coordinates that follow ?c=? are the same as those of this C atom. What follows, as specified before, is the direction of the axis along with to put the pz orbital. These are obtained (more difficult to say than to do it!) by: i) identifying the three first neighbours (manually, for example visualizing the structure with XCrysDen or automatically, by writing some simple script once you understand the algorithm) of the C atom , say P1, P2, P3 ii) compute M1 = (P1 - P2)/Norm[P1 - P2] and M2 = (P1 - P3)/Norm[P1 - P3], these are the versors connecting P1 and P2 and P1 and P3, respectively iii) compute V = (M2 x M3)/Norm[(M2 x M3)], where x = cross product (V is normal to both M2 and M3) iv) because the ideal nanotube surface is such that at each point the normal is always perpendicular to the nanotube axis, get rid of the V component parallel to the nanotube axis, so V? = V - (V . z) z, where . = dot product and z is the versor of the nanotube axis The result is 0.809017, 0.587785, 0., that should answer your question 4. How or why do we choose a specific number of projections? I am assuming it depends on the MLWF and bands that we are interested in but not sure. Yes it depends, generally you should recognise the chemistry of your system and the character (in terms of atomic orbitals or their combinations) of the bands you are interested in (you might what to reproduce only a subset of your band structure, for example group of bands close to the Fermi level). You can tell from my questions that I am totally confused. Any feedback and comments from anyone are greatly appreciated. Apologies for such long email and questions. Looking forward to hearing from you. Many thanks in advance Actually, apart from simple systems, choosing the proper initial guess might be a quite hard task. Giovanni -- Zeina Al-Dolami PhD Candidate Microelectronics and Photonics Graduate Program University of Arkansas Fayetteville, AR 72701 Office: PHYS 244 Email: zaldolam at email.uark.edu _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- 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 _______________________________________________ Wannier mailing list Wannier at quantum-espresso.org http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: From giovanni.cantele at spin.cnr.it Wed Jul 8 22:09:45 2015 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Wed, 8 Jul 2015 22:09:45 +0200 Subject: [Wannier] initial projections In-Reply-To: <-3652220572908964699@unknownmsgid> References: <7A8D000A-1B63-46CF-8971-BA5D2ED4139D@spin.cnr.it> <-3652220572908964699@unknownmsgid> Message-ID: <3FB4171E-BAAE-41A8-AA1C-318DE2861C42@spin.cnr.it> Sorry, I meant M1 and M2! Giovanni > On 08 Jul 2015, at 20:55, Zeina Al-Dolami wrote: > > Dr. Giovanni, > Thanks so much for your nice explanation. I just want to make sure of your answer to question 3. Did you mean M1 and M2 in answer 3 step 3?? What is M3? Thanks again and looking forward to hearing from you > > Zeina > > On Jul 7, 2015, at 4:13 AM, Giovanni Cantele wrote: > >> >>> On 07 Jul 2015, at 09:45, Zeina Al-Dolami wrote: >>> >>> Dear wannier90's owners and developers, >>> I have been trying to understand the examples well before going further. One of the relevant topic that I am having hard time understanding is the initial projections and the best way to define them for a system. I have read the user guide and tutorials to gain more insight. Also, I have found nice details and explanations related to the projections of carbon nano tubes and graphene systems based on the examples provided within wannier90. However, I am totally confused about the way that these projections are found. My questions might be related to the chemistry, but I need your help to start and then go from there. My questions are: >>> >>> 1. Prof.Nicola has mentioned that s-like projections are in the middle of each bond that has to be identified correctly. How to identify them? To clarify, example13 has this projection c= -2.7274, -1.9677, -0.6157 :s . How to find these numbers for the center of projections? Is there mathematical formula or chemistry reasons? How are they found preciously for any system? >> >> This example refers to a carbon nanotube, where the initial guess consists in one pz orbital (with the z axis properly oriented) per each C atom, and one s orbital at each bond. This reflects the chemistry of C-based nanostructures (C nanotubes, graphene), where the sp2 hybridisation occurs. The numbers you mention are the coordinates of the middle point between the atoms >> C -3.151822438 -1.395018907 -0.615700000 >> C -2.303060204 -2.540325691 -0.615700000 >> that are given in input. You find an s orbital at each middle bond. >> >>> >>> 2. One of the pz projections of the same example is c= 3.3780, -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1. The center of CNT is 0,0,0. >>> In the forum, there is an emphasis that the direction of the CNT along z-axis, so z and x are identified to be along z direction. In case CNT is along x, should we have z=0.0,-0.7128, -0.6157 :x=1,0,0 or I am confused by the statement in the forum?? >> >> The carbon nanotube axis, of the mentioned example, is parallel to the z axis. However, for each C atom, the corresponding pz orbital is not parallel to the z axis but orthogonal to the nanotube surface, as the chemistry of a C nanotube tells you. In other words, for each C atom, you must calculate the direction normal to the nanotube and tell wannier90 to use as an initial guess a pz orbital along that direction. Should you have graphene, this problem would not occur, in that case all pz orbital would be parallel to each other. >> >> >>> >>> 3.In example15, one of the pz projections is c=18,1.15042363,0.0:pz:z=0.809016993454,0.587785253559,0.0:x=0,0,1 >>> How to get these numbers z=0.809016993454,0.587785253559,0.0? Is it same way as question 1? >> >> In this case, at variance with question 1, you are looking for a pz guess. The center is on the 1st carbon atom >> C 1.58342228 1.15042363 0.00000000 >> so the coordinates that follow ?c=? are the same as those of this C atom. What follows, as specified before, is the direction of the axis along with to put the pz orbital. >> These are obtained (more difficult to say than to do it!) by: >> i) identifying the three first neighbours (manually, for example visualizing the structure with XCrysDen or automatically, by writing some simple script once you understand the algorithm) of the C atom , say P1, P2, P3 >> ii) compute M1 = (P1 - P2)/Norm[P1 - P2] and M2 = (P1 - P3)/Norm[P1 - P3], these are the versors connecting P1 and P2 and P1 and P3, respectively >> iii) compute V = (M2 x M3)/Norm[(M2 x M3)], where x = cross product (V is normal to both M2 and M3) >> iv) because the ideal nanotube surface is such that at each point the normal is always perpendicular to the nanotube axis, get rid of the V component parallel to the nanotube axis, so V? = V - (V . z) z, where . = dot product and z is the versor of the nanotube axis >> >> The result is 0.809017, 0.587785, 0., that should answer your question >> >> >>> >>> 4. How or why do we choose a specific number of projections? I am assuming it depends on the MLWF and bands that we are interested in but not sure. >> >> Yes it depends, generally you should recognise the chemistry of your system and the character (in terms of atomic orbitals or their combinations) of the bands you are interested in (you might what to reproduce only a subset of your band structure, for example group of bands close to the Fermi level). >> >>> >>> You can tell from my questions that I am totally confused. Any feedback and comments from anyone are greatly appreciated. Apologies for such long email and questions. Looking forward to hearing from you. Many thanks in advance >> >> Actually, apart from simple systems, choosing the proper initial guess might be a quite hard task. >> >> Giovanni >> >>> >>> -- >>> Zeina Al-Dolami >>> PhD Candidate >>> Microelectronics and Photonics Graduate Program >>> University of Arkansas >>> Fayetteville, AR 72701 >>> Office: PHYS 244 >>> Email: zaldolam at email.uark.edu >>> _______________________________________________ >>> Wannier mailing list >>> Wannier at quantum-espresso.org >>> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier >> >> -- >> >> 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 >> >> _______________________________________________ >> Wannier mailing list >> Wannier at quantum-espresso.org >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -- 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 From zaldolam at email.uark.edu Tue Jul 14 08:29:45 2015 From: zaldolam at email.uark.edu (Zeina Al-Dolami) Date: Tue, 14 Jul 2015 01:29:45 -0500 Subject: [Wannier] initial projections In-Reply-To: <3FB4171E-BAAE-41A8-AA1C-318DE2861C42@spin.cnr.it> References: <7A8D000A-1B63-46CF-8971-BA5D2ED4139D@spin.cnr.it> <-3652220572908964699@unknownmsgid> <3FB4171E-BAAE-41A8-AA1C-318DE2861C42@spin.cnr.it> Message-ID: Dr.Giovanni, Thanks again for your response. I have one more question. In case I have a system of 15 carbon atoms. 5 of them are sp hybirdized. Another 5 atoms are sp2 hybirdized and the last 5 are sp3 hybirdized. How can I define their projections? My question may not be realistic, but I just want to have an idea if it is possible and related to what you have explained to me. Thanks in advance and looking forward to hearing from you or anyone who can clarify it to me Regards, Zeina On Wed, Jul 8, 2015 at 3:09 PM, Giovanni Cantele < giovanni.cantele at spin.cnr.it> wrote: > Sorry, I meant M1 and M2! > > Giovanni > > > On 08 Jul 2015, at 20:55, Zeina Al-Dolami > wrote: > > > > Dr. Giovanni, > > Thanks so much for your nice explanation. I just want to make sure of > your answer to question 3. Did you mean M1 and M2 in answer 3 step 3?? What > is M3? Thanks again and looking forward to hearing from you > > > > Zeina > > > > On Jul 7, 2015, at 4:13 AM, Giovanni Cantele < > giovanni.cantele at spin.cnr.it> wrote: > > > >> > >>> On 07 Jul 2015, at 09:45, Zeina Al-Dolami > wrote: > >>> > >>> Dear wannier90's owners and developers, > >>> I have been trying to understand the examples well before going > further. One of the relevant topic that I am having hard time understanding > is the initial projections and the best way to define them for a system. I > have read the user guide and tutorials to gain more insight. Also, I have > found nice details and explanations related to the projections of carbon > nano tubes and graphene systems based on the examples provided within > wannier90. However, I am totally confused about the way that these > projections are found. My questions might be related to the chemistry, but > I need your help to start and then go from there. My questions are: > >>> > >>> 1. Prof.Nicola has mentioned that s-like projections are in the middle > of each bond that has to be identified correctly. How to identify them? To > clarify, example13 has this projection c= -2.7274, -1.9677, -0.6157 :s . > How to find these numbers for the center of projections? Is there > mathematical formula or chemistry reasons? How are they found preciously > for any system? > >> > >> This example refers to a carbon nanotube, where the initial guess > consists in one pz orbital (with the z axis properly oriented) per each C > atom, and one s orbital at each bond. This reflects the chemistry of > C-based nanostructures (C nanotubes, graphene), where the sp2 hybridisation > occurs. The numbers you mention are the coordinates of the middle point > between the atoms > >> C -3.151822438 -1.395018907 -0.615700000 > >> C -2.303060204 -2.540325691 -0.615700000 > >> that are given in input. You find an s orbital at each middle bond. > >> > >>> > >>> 2. One of the pz projections of the same example is c= 3.3780, > -0.7128, -0.6157 :pz :z= 3.3780, -0.7128, 0.0000 :x=0,0,1. The center of > CNT is 0,0,0. > >>> In the forum, there is an emphasis that the direction of the CNT > along z-axis, so z and x are identified to be along z direction. In case > CNT is along x, should we have z=0.0,-0.7128, -0.6157 :x=1,0,0 or I am > confused by the statement in the forum?? > >> > >> The carbon nanotube axis, of the mentioned example, is parallel to the > z axis. However, for each C atom, the corresponding pz orbital is not > parallel to the z axis but orthogonal to the nanotube surface, as the > chemistry of a C nanotube tells you. In other words, for each C atom, you > must calculate the direction normal to the nanotube and tell wannier90 to > use as an initial guess a pz orbital along that direction. Should you have > graphene, this problem would not occur, in that case all pz orbital would > be parallel to each other. > >> > >> > >>> > >>> 3.In example15, one of the pz projections is > c=18,1.15042363,0.0:pz:z=0.809016993454,0.587785253559,0.0:x=0,0,1 > >>> How to get these numbers z=0.809016993454,0.587785253559,0.0? Is it > same way as question 1? > >> > >> In this case, at variance with question 1, you are looking for a pz > guess. The center is on the 1st carbon atom > >> C 1.58342228 1.15042363 0.00000000 > >> so the coordinates that follow ?c=? are the same as those of this C > atom. What follows, as specified before, is the direction of the axis along > with to put the pz orbital. > >> These are obtained (more difficult to say than to do it!) by: > >> i) identifying the three first neighbours (manually, for example > visualizing the structure with XCrysDen or automatically, by writing some > simple script once you understand the algorithm) of the C atom , say P1, > P2, P3 > >> ii) compute M1 = (P1 - P2)/Norm[P1 - P2] and M2 = (P1 - P3)/Norm[P1 - > P3], these are the versors connecting P1 and P2 and P1 and P3, respectively > >> iii) compute V = (M2 x M3)/Norm[(M2 x M3)], where x = cross product (V > is normal to both M2 and M3) > >> iv) because the ideal nanotube surface is such that at each point the > normal is always perpendicular to the nanotube axis, get rid of the V > component parallel to the nanotube axis, so V? = V - (V . z) z, where . = > dot product and z is the versor of the nanotube axis > >> > >> The result is 0.809017, 0.587785, 0., that should answer your question > >> > >> > >>> > >>> 4. How or why do we choose a specific number of projections? I am > assuming it depends on the MLWF and bands that we are interested in but not > sure. > >> > >> Yes it depends, generally you should recognise the chemistry of your > system and the character (in terms of atomic orbitals or their > combinations) of the bands you are interested in (you might what to > reproduce only a subset of your band structure, for example group of bands > close to the Fermi level). > >> > >>> > >>> You can tell from my questions that I am totally confused. Any > feedback and comments from anyone are greatly appreciated. Apologies for > such long email and questions. Looking forward to hearing from you. Many > thanks in advance > >> > >> Actually, apart from simple systems, choosing the proper initial guess > might be a quite hard task. > >> > >> Giovanni > >> > >>> > >>> -- > >>> Zeina Al-Dolami > >>> PhD Candidate > >>> Microelectronics and Photonics Graduate Program > >>> University of Arkansas > >>> Fayetteville, AR 72701 > >>> Office: PHYS 244 > >>> Email: zaldolam at email.uark.edu > >>> _______________________________________________ > >>> Wannier mailing list > >>> Wannier at quantum-espresso.org > >>> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > >> > >> -- > >> > >> 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 > >> > >> _______________________________________________ > >> Wannier mailing list > >> Wannier at quantum-espresso.org > >> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > > -- > > 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 > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier > -- Zeina Al-Dolami PhD Candidate Microelectronics and Photonics Graduate Program University of Arkansas Fayetteville, AR 72701 Office: PHYS 244 Email: zaldolam at email.uark.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From santubaidya2009 at gmail.com Thu Jul 16 15:01:52 2015 From: santubaidya2009 at gmail.com (Santu Baidya) Date: Thu, 16 Jul 2015 18:31:52 +0530 Subject: [Wannier] Wannier90 calculation for a1g or egPi orbitals with local coordianates and band matching Message-ID: Dear Wannier90 users and developers, I am using wannier90 code with wien2k for calculating wannier orbitals corresponding to four bands crossing Fermi level. These four bands come from d orbitals of two ions in the cell. By doing charge density calculation it is confirmed that four bands belong to egPi band. When I plotted wannier functions I do not see orbital shape of egPi orbital. However I see dz2 and dx2-y2 orbital which were given as input to the case.win file. I would like to know if wannier90 capable of showing a1g or egPi type orbitals combination of dxy, dxz, dyz orbitals. My second concern is band matching. For simple structure like SrVO3 band matching is reasonable. But for complex structure even where four bands are separated from other bands wannier90 bands do not match reasonably with total band. Please tell me what should I do in this case. Is it possible to give local coordiantes for band plotting using wannier90? I look forward to receive your reply. Thanking you and with regards, Santu Baidya -------------- next part -------------- An HTML attachment was scrubbed... URL: From jesse.vaitkus at rmit.edu.au Fri Jul 17 01:24:55 2015 From: jesse.vaitkus at rmit.edu.au (Jesse Vaitkus) Date: Fri, 17 Jul 2015 09:24:55 +1000 Subject: [Wannier] Help: Optimising low lying bands for transport calculations Message-ID: Hello Wannier mailing list, I am trying to use Wannier90 to replicate the low lying conduction bands of a very entangled set of bands but I haven't been able to make much progress. I'd like to use them for conduction properties and as such I'd like to get them as correct about that point as possible. As you can see below, the Fermi energy (black line) sits low in the conduction band and as such I only care about bands in the local vicinity; unfortunately the bands are very intertwined (there are several hundred more above the visible axis). DFT calculations were made using a 6x1x1 grid as the amount of padding in the y,z directions should mean that Y and Z are being folded to zero; the corresponding image goes from Gamma to X. Is there any way I can treat them (the lowest two bands) specifically/specially? If I'm not mistaken, when specifying a frozen window it must encompass the entire band which as you can see leads to something like 9 bands being in the frozen window not just the two I'm interested in. In any case, I have done this and the runs do not converge nor do the WF centres make much sense. I would provide some of the output bands/centres but they change greatly from case to case and often don't make any sense at all. If you think Wannier functions are not suited to this particular problem, I am open to suggestions for possible alternatives. [image: Inline images 1] Cheers, Jesse Vaitkus -- ???????????????????????????????? Mr. Jesse Vaitkus MAIP BAppSc(Phys) Hons, BAppSc(Nano) PhD candidate Room 14.6.02 Chemical and Quantum Physics School of Applied Sciences RMIT University Victoria 3001 Australia jesse.vaitkus at rmit.edu.au ???????????????????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bands.png Type: image/png Size: 10892 bytes Desc: not available URL: From giovanni.pizzi at epfl.ch Fri Jul 17 09:56:15 2015 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Fri, 17 Jul 2015 09:56:15 +0200 Subject: [Wannier] Help: Optimising low lying bands for transport calculations In-Reply-To: References: Message-ID: <55A8B51F.3060205@epfl.ch> Dear Jesse, > > Is there any way I can treat them (the lowest two bands) > specifically/specially? If I'm not mistaken, when specifying a frozen > window it must encompass the entire band which as you can see leads to > something like 9 bands being in the frozen window not just the two I'm > interested in. I'm not sure to understand what you mean, but you don't need to freeze the whole band; a suggestion I have is to set the frozen window at (roughly) the Fermi energy, and see if you can converge. Check instead to choose a outer window large enough to include the whole bands (or anyway bands of similar symmetry, even if they are disconnected due to anticrossing). Best, Giovanni -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 340 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31124 On 07/17/2015 01:24 AM, Jesse Vaitkus wrote: > Hello Wannier mailing list, > > I am trying to use Wannier90 to replicate the low lying conduction > bands of a very entangled set of bands but I haven't been able to make > much progress. I'd like to use them for conduction properties and as > such I'd like to get them as correct about that point as possible. > > As you can see below, the Fermi energy (black line) sits low in the > conduction band and as such I only care about bands in the local > vicinity; unfortunately the bands are very intertwined (there are > several hundred more above the visible axis). > > DFT calculations were made using a 6x1x1 grid as the amount of padding > in the y,z directions should mean that Y and Z are being folded to > zero; the corresponding image goes from Gamma to X. > > Is there any way I can treat them (the lowest two bands) > specifically/specially? If I'm not mistaken, when specifying a frozen > window it must encompass the entire band which as you can see leads to > something like 9 bands being in the frozen window not just the two I'm > interested in. > > In any case, I have done this and the runs do not converge nor do the > WF centres make much sense. I would provide some of the output > bands/centres but they change greatly from case to case and often > don't make any sense at all. > > If you think Wannier functions are not suited to this particular > problem, I am open to suggestions for possible alternatives. > > Inline images 1 > > Cheers, > Jesse Vaitkus > > > -- > > ???????????????????????????????? > Mr. Jesse Vaitkus MAIP > BAppSc(Phys) Hons, BAppSc(Nano) > > PhD candidate > Room 14.6.02 > > Chemical and Quantum Physics > School of Applied Sciences > RMIT University > Victoria 3001 > Australia > > jesse.vaitkus at rmit.edu.au > ???????????????????????????????? > > > _______________________________________________ > Wannier mailing list > Wannier at quantum-espresso.org > http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10892 bytes Desc: not available URL: From elias.assmann at gmail.com Fri Jul 17 10:30:52 2015 From: elias.assmann at gmail.com (Elias Assmann) Date: Fri, 17 Jul 2015 10:30:52 +0200 Subject: [Wannier] Wannier90 calculation for a1g or egPi orbitals with local coordianates and band matching In-Reply-To: References: Message-ID: <55A8BD3C.3060305@gmail.com> On 07/16/2015 03:01 PM, Santu Baidya wrote: > I am using wannier90 code with wien2k for calculating wannier > orbitals corresponding to four bands crossing Fermi level. ... > I would like to know if wannier90 capable of showing a1g or egPi > type orbitals combination of dxy, dxz, dyz orbitals. If you are using Wien2k, actually wien2wannier is responsible for the initial projections rather than Wannier90, so this is really a wien2wannier question. The ?write_inwf? utility lets you choose from a number of ?special? combinations of spherical harmonics, but in the ?case.inwf? file, you can make any combination of Ylm's you like [caveat: in the usual basis, not the real-valued one]. > My second concern is band matching. For simple structure like SrVO3 > band matching is reasonable. But for complex structure even where > four bands are separated from other bands wannier90 bands do not > match reasonably with total band. Please tell me what should I do in > this case. I assume you mean the match between Wien2k bands and the Wannier interpolated bands from Wannier90. What you say sounds like you are able to make a Wannier projection without disentanglement [isolated bands]. I can say nothing beyond the usual advice: * Make sure that the bands are properly identified and that you really do not need disentanglement * Choose proper initial projections * Check that the Wannierization was converged * Try more k-points > Is it possible to give local coordiantes for band plotting using > wannier90? I do not know what that means. -- Elias Assmann Wien2Wannier: maximally localized Wannier functions from linearized augmented plane waves