Re: [SIESTA-L] ./optical e2.dat
To respected siesta users, when I run input using ./input SysLabel.EPSIMG and then I write ./optical without the arrow, still the segmentation fault occurs ?!?! What is the reason? Regards, Catrina From: Marty Blaber [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Sunday, December 7, 2008 9:31:38 AM Subject: Re: [SIESTA-L] ./optical e2.dat Hi Catrina, Once you have run input: ../input SysLabel.EPSIMG you need only run optical without the redirect arrow: ../optical This will automatically read the e2.dat file and provide you with the real permittivity and other such things. If you're performing a calculation on metals and you want to add the intraband component of the dielectric function, you can use the following to convert from relaxation time (in seconds ) into hartree's H=6.626068E-34; Elec=1.60217646E-19; PI=3.14159265; eV=((1/$1)*H)/(2*PI*Elec); Har=eV/27.2113845; Cheers, Marty 2008/12/7 catrina desport [EMAIL PROTECTED] To all respected siesta users, I have compiled siesta with gfortran. After compiling optical from utility when I write ./optical e2.dat, I receive segmentation fault. What's the reason for that. Quick responce is really needed. Regards, Catrina
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat
hi, can you run the regular siesta (compiled with gfortran) ? do you still get segfaults..if yes then your compilation may not be correct. s.auluck -- ... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 IndiaE-mail:[EMAIL PROTECTED] FB 480 or 378 [EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ...
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat
Hello, can you run the regular siesta (compiled with gfortran) ? yes I can. I also do not receive segfaults while I compile other .f files in utility, this has occured only for optical what should I change in it to get the run? Regards, Catrina From: Sushil Auluck [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Sunday, December 7, 2008 12:50:24 PM Subject: Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat hi, can you run the regular siesta (compiled with gfortran) ? do you still get segfaults..if yes then your compilation may not be correct. s.auluck -- ... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:[EMAIL PROTECTED] FB 480 or 378 [EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html
Re: [SIESTA-L] [SUSPECTED-SPAM] [SIESTA-L] Question about polarization
Dr. Auluck, Thanks a lot for your response. With this methodology, I end up getting a value of the order of 7 C/m^2 (as opposed to reported value of 1.29 C/m^2). So, I have been wondering about the sources of errors in my input file. A sample is copied at the end of this mail. I studied the affect of polarization grids and they don't seem to make much difference. I am using a DZP basis set, with TM potentials for Zn and O downloaded from SIESTA database (GGA/PBE). Any other ideas on what should I be checking? Regards, Ravi - # Input file - # Crystal System - 6mm (Wurtzite) # Space group - P63mc # Systemname is a name for your conevenience SystemName ZnO Crystal # SystemLabel is used to name the output files accordingly SystemLabel zno NumberOfAtoms 4 NumberOfSpecies 2 MeshCutoff 350 Ry %block ChemicalSpeciesLabel 1 30 Zn # Species index, atomic number, species label 2 8 O %endblock ChemicalSpeciesLabel AtomicCoordinatesFormat Ang LatticeConstant 1.00 Ang MD.TypeofRun FC MD.NumCGsteps 300 SolutionMethod diagon PAO.BasisSize DZP PAO.BasisType split #split, splitgauss, nodes, nonodes %block PolarizationGrids 7 3 3 3 7 3 3 3 7 %endblock PolarizationGrids BornCharge True %block k_grid_Monkhorst_Pack 9 0 0 0. 0 9 0 0. 0 0 7 0 %endblock k_grid_Monkhorst_Pack maxSCFIterations 200 xc.functional GGA xc.authors PBE #for GGA - PBE, revPBE, RPBE, LYP DM.MixingWeight 0.05 DM.NumberPulay 4 DM.NumberBroyden 4 LongOutput T %block LatticeParameters 3.28430 3.28430 5.28815 90 90 60 %endblock LatticeParameters %block AtomicCoordinatesAndAtomicSpecies 1.64200 0.94825 2.64454 1 1.64200 0.94825 4.63445 2 0.0 0.0 0.0 1 0.0 0.0 1.99040 2 %endblock AtomicCoordinatesAndAtomicSpecies On Fri, Dec 5, 2008 at 9:53 PM, Sushil Auluck [EMAIL PROTECTED] wrote: ravi, you are correct. make sure volume is in m^3.. s.auluck Dear SIESTA users, I am trying to do the calculation of piezoelectric coefficients for bulk ZnO with a unit cell consisting of 4 atoms. Coefficient (d33) is calculated as the slope of polarization vs strain curve. Strain is dimensionless and therefore the units of d33 is same as that of polarization. In SIESTA output, the polarization is expressed in Debye units (1 Debye = 3.33 X 10e-30 C-m). To convert it to C/m^2 (standard unit used for d33), I am diving by the volume of the unit cell. Is that correct or am I missing something? Thanks in advance. Ravi ... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 IndiaE-mail:[EMAIL PROTECTED][EMAIL PROTECTED] ...:[EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ... ~
Re: [SIESTA-L] correct optical calculation
Hi Julie, The scissor operator moves all the eigenvalues above the fermi energy (chemical potential) up by the value you specify, this is to compensate for the underestimation of the band gap. Usually you just choose it so that you're band gap matches experiment. The Broadening parameter specifies the size of the gaussian convolved with the transitions, and as such also defines the number of points that appear in the .EPSIMG file. As a rule of thumb you should try to keep the broadening reasonably low. You can always broaden the data further, but you can't deconvolve the gaussian out of the data (because of the correlation between gaussian width and number of points). I generally use a broadening of 0.02 eV. Don't forget that if you're dealing with metals, the plasma frequency converges slower than the transitions, so you should use large optical mesh. Your optical.Mesh should be the same style as you're monkhorst pack grid, but much higher density. To get accurate optical calculations, on gold for example, you should use a monkhorst pack grid of about 21, but you may have to go as high as 29 if you're unit cell is small. %block kgrid_Monkhorst_Pack 21 0 0 0.00 0 21 0 0.00 0 0 21 0.00 %endblock kgrid_Monkhorst_Pack And then use a mesh like this: %block Optical.Mesh 65 65 65 %endblock Optical.Mesh Note that you should test the convergence of these parameters. Also, the finer that your broadening is, the more points you need in optical kspace to get smooth data. The real part is more difficult, if you're using metals, you will have to guess the relaxation time. And you must check the convergence of the plasma frequency with increasing optical mesh. Cheers, MArty 2008/12/7 Julie Smart [EMAIL PROTECTED] Hi all, I have read all mailing archive of Siesta and also all the tutorials and the power points about optical properties. Still I have problem with Optical.Broaden and Optical.Scissor, seems that I have no good idea what they do although forexample I know what gaussian broadening is. To cut it short, I want to know usually what ranges of these two parameters ore suitable for bulk, 1D and 2D structures. Also, when I can get the best shape of imaginary and real part of dielectric function. It would be an honor to receive your advice. Best wishes Julie Smart Caltech University www.*caltech*.edu
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat
Hi Catrina, Do you have any strange numbers in e2.dat are there any NaN's or anything? These should give you an error, but may cause seg fault. Worst case scenario, could you post the e2.dat here. Cheers, Marty 2008/12/7 catrina desport [EMAIL PROTECTED] Hello, can you run the regular siesta (compiled with gfortran) ? yes I can. I also do not receive segfaults while I compile other .f files in utility, this has occured only for optical what should I change in it to get the run? Regards, Catrina -- *From:* Sushil Auluck [EMAIL PROTECTED] *To:* SIESTA-L@listserv.uam.es *Sent:* Sunday, December 7, 2008 12:50:24 PM *Subject:* Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat hi, can you run the regular siesta (compiled with gfortran) ? do you still get segfaults..if yes then your compilation may not be correct. s.auluck -- ... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914India E-mail:[EMAIL PROTECTED] FB 480 or 378 [EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ...
Re: [SIESTA-L] correct optical calculation
Dear Marty, Happy to receive your guide. I have put broadening of 0.2 eV, since when I consider smaller amounts, the imaginary part of dielectric function goes to have alot of ups and downs which changes the results I expect. Should I again try to cgange it to smaller amounts? Also, for 2D structure I have: %block kgrid_Monkhorst_Pack 8 0 0 0.00 0 8 0 0.00 0 0 1 0.00 %endblock kgrid_Monkhorst_Pack So, I have chosen the mesh as: %block Optical.Mesh 40 40 1 %endblock Optical.Mesh should I still change 1 to higher amounts? Also, for the Scissor, as far as I got you we will have optical scissor = experimental bandgap - calculated bandgap ? Wait for your kind advice. Best wishes Julie Smart Caltech University www.caltech.edu From: Marty Blaber [EMAIL PROTECTED] To: SIESTA-L@listserv.uam.es Sent: Monday, December 8, 2008 4:07:18 AM Subject: Re: [SIESTA-L] correct optical calculation Hi Julie, The scissor operator moves all the eigenvalues above the fermi energy (chemical potential) up by the value you specify, this is to compensate for the underestimation of the band gap. Usually you just choose it so that you're band gap matches experiment. The Broadening parameter specifies the size of the gaussian convolved with the transitions, and as such also defines the number of points that appear in the .EPSIMG file. As a rule of thumb you should try to keep the broadening reasonably low. You can always broaden the data further, but you can't deconvolve the gaussian out of the data (because of the correlation between gaussian width and number of points). I generally use a broadening of 0.02 eV. Don't forget that if you're dealing with metals, the plasma frequency converges slower than the transitions, so you should use large optical mesh. Your optical.Mesh should be the same style as you're monkhorst pack grid, but much higher density. To get accurate optical calculations, on gold for example, you should use a monkhorst pack grid of about 21, but you may have to go as high as 29 if you're unit cell is small. %block kgrid_Monkhorst_Pack 21 0 0 0.00 0 21 0 0.00 0 0 21 0.00 %endblock kgrid_Monkhorst_Pack And then use a mesh like this: %block Optical.Mesh 65 65 65 %endblock Optical.Mesh Note that you should test the convergence of these parameters. Also, the finer that your broadening is, the more points you need in optical kspace to get smooth data. The real part is more difficult, if you're using metals, you will have to guess the relaxation time. And you must check the convergence of the plasma frequency with increasing optical mesh. Cheers, MArty 2008/12/7 Julie Smart [EMAIL PROTECTED] Hi all, I have read all mailing archive of Siesta and also all the tutorials and the power points about optical properties. Still I have problem with Optical.Broaden and Optical.Scissor, seems that I have no good idea what they do although forexample I know what gaussian broadening is. To cut it short, I want to know usually what ranges of these two parameters ore suitable for bulk, 1D and 2D structures. Also, when I can get the best shape of imaginary and real part of dielectric function. It would be an honor to receive your advice. Best wishes Julie Smart Caltech University www.caltech.edu
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat
Hi Catrina, The problem with your data file is that it has too many points. (The default limit is 10 000 points) I've edited the optical.f file to allow for 25000 points. you can compile it using gfortran -O4 optical.f -o optical the O4 makes the calculation much faster. The program should have stopped with an error saying Too many points but this doesn't always work I'll email the result to you personally because I don't think the list accepts attachments that are very big. Cheers, Marty 2008/12/8 catrina desport [EMAIL PROTECTED] Hello Marty, Thank you for helping me. I didn't find Nan's in e2.file, you can see it in the enclosed. I would be thankful to see what is going wrong. Regards, Catrina -- ** optical.tar.gz Description: GNU Zip compressed data
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical e2.dat
hi, normally energy eigenvalues ( from linear methods) are supposed to be reliable to within 1 Ry of the fermi energy. so you would expect that e2 to be ok for up to 1 Ry. suppose you have 1000 energy eigenvalues in this range, then the spacing (dE) is about 2/1000 = 0.002 Ry. Broadening could be 0.004 or even larger. experiments normally have an accuracy of about 0.05 eV which is 0.004 Ry...these are rough estimates. s.auluck -- ... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 IndiaE-mail:[EMAIL PROTECTED] FB 480 or 378 [EMAIL PROTECTED] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ...
