Re: [Wien] Reg: BerryPI calculation
You can create non equivalent atoms using the w2web interface. You have to use the split options to divide the two equivalent positions of Atom 1 into two different atoms. And then label them as 1 and 2 which will make sure that the symmetry operation doesn't realize that you have two equivalent positions. Then you can go on to compute the effective charge for atom 1. Alternatively, on your current structure both the atoms are equivalent which means they will have the same effective charge. So, I would suggest that instead of displacing just one atomic positions if you use identical displacement for the both positions, you can compute sum of the effective charges for the two equivalent atoms without any errors. Then you just have to average them. PS: make sure that you lattice vectors are orthogonal. BerryPI doesn't yet have the capability to compute polarization for non orthogonal case. Hope that will help. Sheikh On Sun, Oct 13, 2013 at 5:26 AM, Shwetha Gummula shwetha.gumm...@gmail.comwrote: Dear Wien2k users and developers, I want to calculate the Born effective charges by using the BerryPI code which is in interface with the wien2k. I have successfully installed and ran the examples. In order to calculate the Born effective charges of particular atom in particular direction we have the change the position of that particular element in the particular direction. But my question is for my compound which is tetragonal structure (ABO4 type), for particular atom A it created equivalent atoms. Ex:ATOM -1: X=0. Y=0.7500 Z=0.3750 MULT= 2 ISPLIT=-2 -1: X=0. Y=0.2500 Z=0.6250 A NPT= 781 R0=0.0500 RMT=2.1200 Z: if i change the position of one atom while initializing it is giving error about the other equivalent position where there position also have to change. Ex:ATOM -1: X=0. Y=0.7500 Z=0.3650 MULT= 2 ISPLIT=-2 -1: X=0. Y=0.2500 Z=0.6250 A NPT= 781 R0=0.0500 RMT=2.1200 Z: In order to change the position (or perturb) do i have to create the again in w2web page with the perturbed positions (A (0 0.75, 0.365)). What will be the correct procedure. How to create the non equivalent positions for every element so that we can easily perturb the positions. please can anyone help me regarding this. Thanking you ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Born effective charge in GaN
Hello Shahrbano, I was able to compute the Effective charge of GaN using the structure files provided by Dr. Rubel. This is how it looks, Z=(1.76267778062-1.7075251678616241)/0.02 Z=2.7576306379187954 My computed effective charge seems to almost the same as computed by Dr. Rubel. I think you are using older versions of either BerryPI or Wien2Wannier or both. Please use the latest version of BerryPI (v1.0) https://github.com/spichardo/BerryPI and Wien2Wannier (v0.97) http://www.wien2k.at/reg_user/unsupported/wien2wannier/. The older version of BerryPI (v0.1) had some problem in wrapping of phases which has been fixed in version 1.0. Also, the older versions of Wien2wannier was having an issue in identifying the complex calculation (see the post http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac. at/msg09119.html) Regards Sheikh On Mon, Nov 4, 2013 at 5:13 PM, Oleg Rubel oru...@lakeheadu.ca wrote: Dear Shahrbano, I was able to obtain the effective charge of Z(Ga) = 2.76 Here is the approach: 1) Take the structure files enclosed (I assume they are not different from yours). 2) create directories 'lambda1' and 'lambda2'. In both cases I displace the Ga atom by +0.01 and -0.01 along z-axis. There is nothing specific about the choice of displacements. In fact 0.005 should work too. I encourage you to test the convergence and plot Z as a function of displacement. I do not recommend to go for displacements larger than 0.01 3) initialize both using 'init_lapw -b -vxc 13 -ecut -6 -numk 230' 4) rum wien2k 'run_lapw' 5) run berrypi 'berrypi -p$(pwd) -k6:6:4'. You should obtain the output as shown below. 6) Z = (1.7626777806241982 - 1.7075447765644145)/(0.01+0.01) = 2.76 (see Eq. 14 in http://www.tbrri.com/~orubel/publications/2013/Ahmed_CPC_ 184_2013.pdf) The result really close to Vanderbilt. Good sign :) In order to address the spontaneous polarization, we need two cases: (a) the initial reference structure and (b) your relaxed structure. The spontaneous polarization is the difference between them. Please, look in the literature what is used as a reference structure. The choice of structure (a) for GaN is not obvious to me. Once you determine that, I can help you to move on. Thank you Oleg +++ ---PHASES/2*PI IN [0 to 2]RANGE--- IONIC PHASE/(2*PI): [6.010209219198259e-08, 1.999400510458, 0.8898641300788697] ELECTRONIC PHASE/(2*PI): [2.35665164408, -3.5664951224354753e-05, 0.87281365054532878] TOTAL PHASE/(2*PI): [3.572526650019725e-05, 1.642750998212, 1.7626777806241982] ---POLARIZATION IN C/m^2 FOR [0 to 2] PHASE/2PI RANGE--- IONIC POLARIZATION:[6.734131068339737e-08, 2.2408973201721545, 1.6229398446248238] ELECTRONIC POLARIZATION:[2.2409373483287527, -3.9960748009166113e-05, 1.5918430719045986] TOTAL POLARIZATION:[4.0028328181192241e-05, 2.2408573594241452, 3.2147829165294222] ---PHASES/2*PI IN [-1 to +1]RANGE--- IONIC PHASE/(2*PI):[6.010209219198259e-08, -5.994895424521474e-08, 0.8898641300788697] ELECTRONIC PHASE/(2*PI):[3.5665164408005268e-05, -3.5664951224312347e-05, 0.87281365054532878] TOTAL PHASE/(2*PI):[3.572526650019725e-05, -3.5724900178779606e-05, -0.23732221937580178] ---POLARIZATION IN C/m^2 FOR [-1 to +1] PHASE/2PI RANGE--- IONIC POLARIZATION:[6.734131068339736e-08, -6.716972747098987e-08, 1.6229398446248238] ELECTRONIC POLARIZATION:[3.9960986870508846e-05, -3.9960748009118604e-05, 1.5918430719045986] TOTAL POLARIZATION:[4.0028328181192241e-05, -4.0027917736838375e-05, -0.432829768973433] + ---PHASES/2*PI IN [0 to 2]RANGE--- IONIC PHASE/(2*PI): [6.010209219198259e-08, 1.999400510458, 0.6298641300758288] ELECTRONIC PHASE/(2*PI): [-2.9599378548340341e-05, 2.295996358957, 1.0776806464885857] TOTAL PHASE/(2*PI): [1.704607235438, 2.9539686940971421e-05, 1.7075447765644145] ---POLARIZATION IN C/m^2 FOR [0 to 2] PHASE/2PI RANGE--- IONIC POLARIZATION:[6.734131068339737e-08, 2.2408973201721545, 1.1487501955039068] ELECTRONIC POLARIZATION:[-3.3164585027959612e-05, 2.2409305522152549, 1.9654807985263416] TOTAL POLARIZATION:[2.2408642900981648, 3.3097703644459985e-05, 3.1142309940302484] ---PHASES/2*PI IN [-1 to +1]RANGE--- IONIC PHASE/(2*PI):[6.010209219198259e-08, -5.994895424521474e-08, 0.6298641300758288] ELECTRONIC PHASE/(2*PI):[-2.9599378548406108e-05, 2.9599635895660725e-05, -0.92231935351141425] TOTAL PHASE/(2*PI):
Re: [Wien] berryphase
Hello Shahrbano, If check the refereed post you find the following about the compatibility issue of WIEN2k v12 or later with WIEN2WANNIER v0.96 or older We came across a minor compatibility issue between WIEN2WANNIER and a newer version Wien2k (v12 and above). Apparently, the complex calculation is not resolved properly by w2w. The following line in 'w2w' script searches for a pattern lapw1 -c in a dayfile tmp=$(grep lapw1 -c $SEEDNAME.dayfile) However, the number of spaces between 'lapw1' and '-c' has changes in wien2k while going from v11 to v12 and higher. As a result, the complex calculation is not identified properly. I suggest to change the line to the following (note the space between 1 and *) tmp=$(grep lapw1 *-c $SEEDNAME.dayfile) This code is compatible with any number of spaces. The modification is absolutely critical for proper calculation of polarization with BerryPi. = That was the compatibility issue taken from http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09119.html Another source of error could be from the older version of BerryPI which was using a different phase wrapping method. That was causing some issues to bring the phases between 0 to 2*pi or -pi to +pi range when some of the phases were close to 0 (may be positive or negative). The method was completely ignoring those smaller values instead of unwarpping all the phases to same range. As a result, you would have phase values like 1.999*pi 1.6*pi 1.9994*pi *-0.0001*pi* instead of 1.999*pi 1.6*pi 1.9994*pi *1.*pi.* This would have messed up your average phase value and polarization. Also regarding the Numpy version, We actually haven't tested BerryPI any Numpy older than v1.6.2. This is why the init.sh tries to ignore the older versions. Hope this will help. Sheikh On Wed, Nov 27, 2013 at 2:14 PM, Shahrbano Raheme sbh6...@yahoo.com wrote: Dear Prof. Rubel and Prof. Sheikh, 1) Take the structure files enclosed (I assume they are not different from yours). I used your stature file and found that it is identical to my structure. Please, make sure that you have the latest version of WIEN2WANNIER (see the post http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09119.htmlhttps://mail.google.com/mail/%22 ). My computed effective charge seems to almost the same as computed by Dr. Rubel. I think you are using older versions of either BerryPI or Wien2Wannier or both. Please use the latest version of BerryPI (v1.0) https://github.com/spichardo/BerryPIhttps://github.com/spichardo/BerryPI%22%20%5Ct%20%22_blank and Wien2Wannier (v0.97) http://www.wien2k.at/reg_user/unsupported/wien2wannier/http://www.wien2k.at/reg_user/unsupported/wien2wannier/%22%20%5Ct%20%22_blank .The older version of BerryPI (v0.1) had some problem in wrapping of phases which has been fixed in version 1.0. Also, the older versions of Wien2wannier was having an issue in identifying the complex calculation (see the post http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09119.htmlhttp://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09119.html%22%20%5Ct%20%22_blank ) I installed the latest version of BerriPI, WIEN2WANNIER, WANNIER90, NUMPHY, and could reproduce the results of Prof. Rubel in agreement with reported values in literature. But, we still do not know what was the source of problem of the BerryPI or WIEN2WANNIER old version which resulted in an unsatisfactory result. We are interested in realizing the bug(s) of the old version(s). 2) create directories 'lambda1' and 'lambda2'. In both cases I displace the Ga atom by +0.01 and -0.01 along z-axis. There is nothing specific about the choice of displacements. In fact 0.005 should work too. I encourage you to test the convergence and plot Z as a function of displacement. I do not recommend to go for displacements larger than 0.01 I did it, and the results which nicely confirm your prediction, do not depend on the Z. Now I am working on your following comments: In order to address the spontaneous polarization, we need two cases: (a) the initial reference structure and (b) your relaxed structure. The spontaneous polarization is the difference between them. Please, look in the literature what is used as a reference structure. The choice of structure (a) for GaN is not obvious to me. Once you determine that, I can help you to move on. Would you give me some clue to reach the goal sooner? PS: We detected that init.sh ha a bug. If the version of the installed numpy is 1.6.2, the init.sh works fine. But, if the version is different depending on the linux version, e.g., numpy 1.4.1, then init.sh script tries to install numpy 1.6.2 on .local directory. This is not necessary, as already bumpy 1.4.1 is installed. Although the installation on .local directory is
Re: [Wien] berryphase
Hello Shahrbano, I also agree with Dr. Rubel that this fraction of discrepancy that you are getting is probably due to the fact we made this tutorial on Wien2k version 11.0. Regarding the forces for optimizing the structure, I always try to optimize my structure to a much lower value (0.2 mRy/bohr) of forces. However, this doesn't make much of a difference to the final result though. Compared to the optimized structure with default force tolerance (2 mRy/bohr), the atomic positions varies only in fourth or fifth decimal places which might change your polarization by 0.1 to 1 % (like you are getting). This is negligible if you are consistent when comparing properties between two calculations. Either use 2 mRy/bohr for both the cases or 0.2 mRy/bohr. Also you can try to understand more about modern theory of polarization from here http://www.physics.rutgers.edu/~dhv/pubs/local_preprint/dv_fchap.pdf Hope that helps. Sheikh On Thu, Dec 5, 2013 at 11:56 AM, Oleg Rubel oru...@lakeheadu.ca wrote: Dear Shahrbano, ... Although we could reproduce the SP of the sample, P_s= P_z(lambda1)- P_z(lambda0) = 0.312113863793- 1.52399256575e-11 = 0.31211386360 C/m^2 which is very close to the readme file (but not exactly the same as it P_s= P_z(lambda1)- P_z(lambda0)= 0.31140111708550217-1.4486341471349937e-11= 0.3114011170710158 C/m^2), there are some things which are not clear for us. This difference is not material. Tutorials were done with an earlier version of Wien2k and a default SCF convergence. Possibly, a tighter convergence will lead to the same result in both cases. Why would not define the P_s just as P_z(lambda1)? In general, P(lambda0) = 0 may not always be true due to pi rapping. So it will be a very slippery assumption. This is why I would insist on doing both calculations (lambda0, lambda1) even though you might expect zero. We examined these two structures by calculating the exerted forces on the atoms of them to check whether they are in their relaxed positions or not. We found that the displaced atoms in lambda1.strcut were under tension--:FOR002 and :FGL002 are not zero. Are there total or partial forces? What are the values? In the way as discussed in tutorial1, the SP certainly will depend on the displacements. If we increase the amount of displacement, then we will obtain larger SP. In any case, you are need a well converged atomic positions. In our calculations we try to optimize structure to better than 2 mRy/Bohr. (Sheikh can probably comment more.) So, unlike Boron effective charge calculations it appears that the SP calculations cannot give a unique result? Indeed, the SP should be unique. There should be only one well converged structure. Of course, it will be sensitive to the choice of XC functional. 3) And, why we should not fully initialize the centrosymmetric one? We do not want Wien2k to realize its higher symmetry. Therefore, the initialization is done for low-symmetry lambda1 case only. Both structures should have identical symmetry operations in order to ensure consistency and comparability of the results. In summary, according to the definition of SP, a transient from a centrosymmetry to a noncentrosymmetry seems to be necessary. But, here both of the phases are tetragonal, while in the paper one of them is considered to be cubic. Strictly speaking, you are right. We would need a cubic structure for lambda0 and you can try it. What you will find in this case that it does not matter for P(lambda0). Where is the transition in this tutorial? You can make a transition by choosing an intermediate structure (say lambda05). I am not aware of unique way to define the intermediate state: we know for sure only lambda0 and lambda1. But you can imagine lambda1 as a distorted case of lambda0. For lambda05 you need half of the distortions. Of course, NO optimization of atomic positions should be performed for lambda05. Otherwise you will end up with lambda1 again. What will be the criterion to move up the atoms? Zero force and stress for lambda1. What is the difference between SP and total polarization? It is the essence of the modern polarization theory that the total polarization does not make sense. Only a difference matters, i.e. SP. Would you discuss how we can find the centrosymmetric and noncentrosymmetric ones for any cases? This part I am not sure, especially for GaN. The thinking should start with analysis of measurable quantities/effects, which you would like to model. Thank you Oleg ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at
Re: [Wien] berryPI
I would like to add that EuTiO3 seems to be a multiferroic compound with ground state being antiferromagnetic- paraelectric system (I4/mcm). Then, under some compressive or tensile epitaxial strain, several types of transition is possible (For example, antiferromagnetic- ferroelectric or ferromagnetic- ferroelectric) depending on the magnitude and type of strain. The following articles address this issue very well. http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.267602 http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.267602 Hope that helps. Sheikh -- Sheikh Jamil Ahmed PhD Student Department of Material Science and Engineering McMaster University 1280 Main Street West Hamilton, Ontario, Canada L8S 4L7 On Tue, Sep 8, 2015 at 3:07 PM, Oleg Rubel <oru...@lakeheadu.ca> wrote: > To address your questions... > > > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and it > helped me very much. So I conclude to calculate the difference in > polarization, two structures that at least one of them should not be > centrosymmetric are needed, Is it correct? > > That’s correct. When the structure file contains the inversion symmetry, > Wien2k switches from complex to real version for wave functions. Then there > is no phase information to be processed. > > > Would you please guide me whether it is allowed to calculate the > difference in polarization between a strained and unstrained state of a > system by implementing the berryPI on each of them separately and then > subtract them ?! if it going to, what does the derived polarization > describe?! Piezoelectricity(since it is the difference in polarization > caused by strain) or spontaneous polarization? > > You are heading towards piezoelectric coefficients. There are some > technicalities, such as clamped vs relaxed ion approximation, proper vs > improper. Here is a good reference: > http://arxiv.org/pdf/cond-mat/9903137.pdf > I do not see any barriers from BerryPI perspective. > > > Best regards > Oleg > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] berryPI
Dear Gerhard, If I understand correctly, the assumption about the structures of EuTiO3 in PhysRevLett.97.267602 is not accurate enough. The only consider the ground state to be Pm3_m and then do a compression study with P4/mm. PhysRevLett.109.267602 on the other hand pointed that the structure of bulk EuTiO3 in ground state should be I4/mcm. Then, under compression the transition goes from I4/mcm to I4cm to P4mm. Sheikh On Wed, Sep 9, 2015 at 5:24 AM, Fecher, Gerhard <fec...@uni-mainz.de> wrote: > If you check Figure 2 of PhysRevLett.109.267602, you will find that there > is NO polarization in I4/mcm ! > and in the PhysRevLett.97.267602 you find "... the crystallographic > symmetry becomes P4/mm", now compare this to the Fig.2 of the first > reference, what do you see ? > > > Ciao > Gerhard > > DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: > "I think the problem, to be quite honest with you, > is that you have never actually known what the question is." > > > Dr. Gerhard H. Fecher > Institut of Inorganic and Analytical Chemistry > Johannes Gutenberg - University > 55099 Mainz > and > Max Planck Institute for Chemical Physics of Solids > 01187 Dresden > > Von: wien-boun...@zeus.theochem.tuwien.ac.at [ > wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Sheikh Jamil > Ahmed [sahm...@lakeheadu.ca] > Gesendet: Dienstag, 8. September 2015 23:06 > An: A Mailing list for WIEN2k users > Betreff: Re: [Wien] berryPI > > I would like to add that EuTiO3 seems to be a multiferroic compound with > ground state being antiferromagnetic- paraelectric system (I4/mcm). Then, > under some compressive or tensile epitaxial strain, several types of > transition is possible (For example, antiferromagnetic- ferroelectric or > ferromagnetic- ferroelectric) depending on the magnitude and type of > strain. The following articles address this issue very well. > http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.267602 > > http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.267602 > > > Hope that helps. > > Sheikh > > -- > Sheikh Jamil Ahmed > PhD Student > Department of Material Science and Engineering > McMaster University > 1280 Main Street West > Hamilton, Ontario, Canada L8S 4L7 > > > On Tue, Sep 8, 2015 at 3:07 PM, Oleg Rubel <oru...@lakeheadu.ca oru...@lakeheadu.ca>> wrote: > To address your questions... > > > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and it > helped me very much. So I conclude to calculate the difference in > polarization, two structures that at least one of them should not be > centrosymmetric are needed, Is it correct? > > That’s correct. When the structure file contains the inversion symmetry, > Wien2k switches from complex to real version for wave functions. Then there > is no phase information to be processed. > > > Would you please guide me whether it is allowed to calculate the > difference in polarization between a strained and unstrained state of a > system by implementing the berryPI on each of them separately and then > subtract them ?! if it going to, what does the derived polarization > describe?! Piezoelectricity(since it is the difference in polarization > caused by strain) or spontaneous polarization? > > You are heading towards piezoelectric coefficients. There are some > technicalities, such as clamped vs relaxed ion approximation, proper vs > improper. Here is a good reference: > http://arxiv.org/pdf/cond-mat/9903137.pdf > I do not see any barriers from BerryPI perspective. > > > Best regards > Oleg > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
